Recombinant viral vectors

ABSTRACT

The present relation relates to recombinant vesicular stomatitis virus for use as prophylactic and therapeutic vaccines for infectious diseases of AIDS. The present invention encompasses the preparation and purification of immunogenic compositions which are formulated into the vaccines of the present invention.

INCORPORATION BY REFERENCE

This application is a Continuation of U.S. application Ser. No.15/663,867 filed Jul. 31, 2017, now U.S. Pat. No. 10,202,424, which is aContinuation of U.S. application Ser. No. 14/972,272 filed Dec. 17,2015, now U.S. Pat. No. 9,802,986, which is a Continuation of U.S.application Ser. No. 12/708,940 filed Feb. 19, 2010, abandoned, andclaims the benefit of priority to U.S. Provisional Patent ApplicationNo. 61/154,190 filed Feb. 20, 2009.

The foregoing applications, and all documents cited therein or duringtheir prosecution (“appln cited documents”) and all documents cited orreferenced herein (“herein cited documents”), and all documents cited orreferenced in herein cited documents, together with any manufacturer'sinstructions, descriptions, product specifications, and product sheetsfor any products mentioned herein or in any document incorporated byreference herein, are hereby incorporated herein by reference, and maybe employed in the practice of the invention.

FEDERAL FUNDING LEGEND

This invention was supported, in part, by NIH grant number:R01-A1084840. The federal government may have certain rights to thisinvention.

SEQUENCE LISTING

The instant application contains a Sequence Listing which has beensubmitted via electronically and is hereby incorporated by reference inits entirety. Said ASCII copy, created on Jun. 9, 2017, is named43094022009.txt and is 16,852 bytes in size.

FIELD OF THE INVENTION

The present invention relates to recombinant vesicular stomatitis virusfor use as prophylactic and therapeutic vaccines for infectious diseasesof AIDS.

BACKGROUND OF THE INVENTION

AIDS, or Acquired Immunodeficiency Syndrome, is caused by humanimmunodeficiency virus (HIV) and is characterized by several clinicalfeatures including wasting syndromes, central nervous systemdegeneration and profound immunosuppression that results inopportunistic infections and malignancies. HIV is a member of thelentivirus family of animal retroviruses, which include the visna virusof sheep and the bovine, feline, and simian immunodeficiency viruses(SIV). Two closely related types of HIV, designated HIV-1 and HIV-2,have been identified thus far, of which HIV-1 is by far the most commoncause of AIDS. However, HIV-2, which differs in genomic structure andantigenicity, causes a similar clinical syndrome.

An infectious HIV particle consists of two identical strands of RNA,each approximately 9.2 kb long, packaged within a core of viralproteins. This core structure is surrounded by a phospholipid bilayerenvelope derived from the host cell membrane that also includesvirally-encoded membrane proteins (Abbas et al., Cellular and MolecularImmunology, 4th edition, W.B. Saunders Company, 2000, p. 454). The HIVgenome has the characteristic 5′-LTR-Gag-Pol-Env-LTR-3′ organization ofthe retrovirus family. Long terminal repeats (LTRs) at each end of theviral genome serve as binding sites for transcriptional regulatoryproteins from the host and regulate viral integration into the hostgenome, viral gene expression, and viral replication.

The HIV genome encodes several structural proteins. The gag gene encodesstructural proteins of the nucleocapsid core and matrix. The pol geneencodes reverse transcriptase (RT), integrase (IN), and viral protease(PR) enzymes required for viral replication. The tat gene encodes aprotein that is required for elongation of viral transcripts. The revgene encodes a protein that promotes the nuclear export of incompletelyspliced or unspliced viral RNAs. The vif gene product enhances theinfectivity of viral particles. The vpr gene product promotes thenuclear import of viral DNA and regulates G2 cell cycle arrest. The vpuand nef genes encode proteins that down regulate host cell CD4expression and enhance release of virus from infected cells. The envgene encodes the viral envelope glycoprotein that is translated as a160-kilodalton (kDa) precursor (gp160) and cleaved by a cellularprotease to yield the external 120-kDa envelope glycoprotein (gp120) andthe transmembrane 41-kDa envelope glycoprotein (gp41), which arerequired for the infection of cells (Abbas, pp. 454-456). gp140 is amodified form of the Env glycoprotein, which contains the external120-kDa envelope glycoprotein portion and the extracellular part of thegp41 portion of Env and has characteristics of both gp120 and gp41. Thenef gene is conserved among primate lentiviruses and is one of the firstviral genes that is transcribed following infection. In vitro, severalfunctions have been described, including down-regulation of CD4 and MHCclass I surface expression, altered T-cell signaling and activation, andenhanced viral infectivity.

HIV infection initiates with gp120 on the viral particle binding to theCD4 and chemokine receptor molecules (e.g., CXCR4, CCR5) on the cellmembrane of target cells such as CD4⁺ T-cells, macrophages and dendriticcells. The bound virus fuses with the target cell and reversetranscribes the RNA genome. The resulting viral DNA integrates into thecellular genome, where it directs the production of new viral RNA, andthereby viral proteins and new virions. These virions bud from theinfected cell membrane and establish productive infections in othercells. This process also kills the originally infected cell. HIV canalso kill cells indirectly because the CD4 receptor on uninfectedT-cells has a strong affinity for gp120 expressed on the surface ofinfected cells. In this case, the uninfected cells bind, via the CD4receptor-gp120 interaction, to infected cells and fuse to form asyncytium, which cannot survive. Destruction of CD4⁺ T-lymphocytes,which are critical to immune defense, is a major cause of theprogressive immune dysfunction that is the hallmark of AIDS diseaseprogression. The loss of CD4⁺ T cells seriously impairs the body'sability to fight most invaders, but it has a particularly severe impacton the defenses against viruses, fungi, parasites and certain bacteria,including mycobacteria.

Research on the Env glycoprotein has shown that the virus has manyeffective protective mechanisms with few vulnerabilities (Wyatt &Sodroski, Science. 1998 Jun. 19; 280(5371):1884-8). For fusion with itstarget cells, HIV-1 uses a trimeric Env complex containing gp120 andgp41 subunits (Burton et al., Nat Immunol. 2004 March; 5(3):233-6). Thefusion potential of the Env complex is triggered by engagement of theCD4 receptor and a coreceptor, usually CCRS or CXCR4. Neutralizingantibodies seem to work either by binding to the mature trimer on thevirion surface and preventing initial receptor engagement events, or bybinding after virion attachment and inhibiting the fusion process(Parren & Burton, Adv Immunol. 2001;77:195-262). In the latter case,neutralizing antibodies may bind to epitopes whose exposure is enhancedor triggered by receptor binding. However, given the potential antiviraleffects of neutralizing antibodies, it is not unexpected that HIV-1 hasevolved multiple mechanisms to protect it from antibody binding (Johnson& Desrosiers, Annu Rev Med. 2002; 53:499-518).

There remains a need to express immunogens that elicit broadlyneutralizing antibodies. Strategies include producing molecules thatmimic the mature trimer on the virion surface, producing Env moleculesengineered to better present neutralizing antibody epitopes thanwild-type molecules, generating stable intermediates of the entryprocess to expose conserved epitopes to which antibodies could gainaccess during entry and producing epitope mimics of the broadlyneutralizing monoclonal antibodies determined from structural studies ofthe antibody-antigen complexes (Burton et al., Nat Immunol. 2004 March;5(3):233-6). However, none of these approaches have yet efficientlyelicited neutralizing antibodies with broad specificity.

Citation or identification of any document in this application is not anadmission that such document is available as prior art to the presentapplication.

SUMMARY OF THE INVENTION

The current invention is based, in part, on Applicant's discovery thatHIV gp41 epitopes known to elicit broadly neutralizing antibodiesinserted into a viral glycoprotein are recognized by such broadlyneutralizing antibodies in cells infected with the recombinant virusexpressing the viral glycoprotein.

Recombinant viruses are viruses generated by introducing foreign geneticmaterial into the genome of the virus. The genome of a virus cancomprise either DNA or RNA. The genome of an RNA virus can be furthercharacterized to be either positive-sense (plus-strand) ornegative-sense (minus-strand). A plus-strand (5′ to 3′) viral RNAindicates that a particular viral RNA sequence can be directlytranslated into the desired viral proteins whereas a minus-strand (3′ to5′) viral RNA must be first converted to a positive-sense by an RNApolymerase prior to translation.

In a first embodiment, the invention relates to a recombinant vesicularstomatitis virus (VSV) vector wherein the gene encoding the VSV surfaceglycoprotein G (VSV G) may be functionally replaced by HIV Env. The HIVEnv may be recognized by antibodies PG9, PG16, 2G12, b12, 2F5, 4E10 orZ13 or other antibodies, including potent broadly neutralizingtrimer-specific antibodies. VSV is a minus-strand RNA virus that caninfect insects and mammals.

In a second embodiment, the invention relates to a recombinant vesicularstomatitis virus (VSV) vector encoding a modified form of VSV G, whereinthe modified form of VSV G may harbor epitopes from the HIV Env membraneproximal external region (MPER). The MPER sequence may be inserted intothe membrane proximal region or other domains of VSV G. The G-MPERprotein may bind with high avidity to 2F5, 4E10 or other monoclonalantibodies.

In a third embodiment, the invention relates to a recombinant vesicularstomatitis virus (VSV) vector encoding a an N-terminally truncated formof VSV G (G/Stem), wherein the G/Stem may display Env epitope sequenceson the surface of VSV particles. The G/Stem may contain a cytoplasmictail (CT) and trans-membrane (TM) spanning domains of G, a 16- to68-amino acid membrane proximal extracellular polypeptide (the Stem),wherein HIV Env epitopes are appended to or inserted into the Stem. TheHIV Env epitopes may be derived from the gp41 MPER or other regions ofEnv. The G/Stem-HIV Env epitope molecules may bind to 2F5, 4E10 or othermonoclonal antibodies with high affinity.

In a fourth embodiment, the invention relates to a method of generatingnovel chimeric HIV Env-VSV G (EnvG) molecules expressed and incorporatedinto VSV which may comprise:

-   -   (a) serially passaging replication-competent chimeric VSV-HIV        viruses that lack the capacity to encode wild-type G and are        dependent on Env or chimeric EnvG molecules for infection and        propagation on cells to promote emergence of viruses with        greater replicative fitness and    -   (b) identifying novel mutations that enhance Env or EnvG        function in VSV-HIV viruses.

The cells may be CD4/CCR5⁺ cells. The novel mutations may escalatetrimer abundance on the virus particle and/or increase the stability ofthe functional trimeric form of Env or EnvG. The method may furthercomprise determining whether the Env or EnvG immunogens elicit broadlyneutralizing anti-Env antibodies.

In a fifth embodiment, the invention relates to method of applyingselective pressure to generate novel Env, EnvG, or G/Stem-antigenchimeras molecules expressed and incorporated into VSV, wherein theselective pressure may be binding to an antibody of interest, therebyenriching for molecules that may be more immunogenic. The antibody maybe 2F5, 4E10, or other Env-specific antibodies.

The present invention also encompasses methods of producing or elicitingan immune response which may comprise administering to a mammal any oneof the herein disclosed recombinant VSV vectors.

The present invention also encompasses other plus and minus strandviruses which can be used as recombinant viral vectors in the method ofthe invention. Such viruses include but are not limited to: Measlesvirus, Canine distemper virus, Parainfluenza viruses, Sendai virus,Newcastle disease virus, Venezuelan equine encephalitis virus, Sindbisvirus, Semliki Forrest virus etc.

Accordingly, it is an object of the invention to not encompass withinthe invention any previously known product, process of making theproduct, or method of using the product such that Applicants reserve theright and hereby disclose a disclaimer of any previously known product,process, or method. It is further noted that the invention does notintend to encompass within the scope of the invention any product,process, or making of the product or method of using the product, whichdoes not meet the written description and enablement requirements of theUSPTO (35 U.S.C. § 112, first paragraph) or the EPO (Article 83 of theEPC), such that Applicants reserve the right and hereby disclose adisclaimer of any previously described product, process of making theproduct, or method of using the product.

It is noted that in this disclosure and particularly in the claimsand/or paragraphs, terms such as “comprises”, “comprised”, “comprising”and the like can have the meaning attributed to it in U.S. Patent law;e.g., they can mean “includes”, “included”, “including”, and the like;and that terms such as “consisting essentially of” and “consistsessentially of” have the meaning ascribed to them in6 U.S. Patent law,e.g., they allow for elements not explicitly recited, but excludeelements that are found in the prior art or that affect a basic or novelcharacteristic of the invention.

These and other embodiments are disclosed or are obvious from andencompassed by, the following Detailed Description.

BRIEF DESCRIPTION OF THE DRAWINGS

The patent or application file contains at least one drawing executed incolor. Copies of this patent or patent application publication withcolor drawing(s) will be provided by the Office upon request and paymentof the necessary fee.

The following detailed description, given by way of example, but notintended to limit the invention solely to the specific embodimentsdescribed, may best be understood in conjunction with the accompanyingdrawings, in which:

FIGS. 1A and 1B depict the HIV-1 envelope protein. A. Illustration ofthe gp160 precursor, which is post-translationally cleaved into thegp120 and gp41 subunits. The locations of the signal and fusionpeptides, the Membrane-Proximal External Region (MPER) and thetransmembrane (TM) segment are indicated. The ruler denotes amino acidnumbering. B. Broadly neutralizing antibodies directed against Env: PG9and PG16 interacts with conserved residues in the V2 and V3 loops andpresent an accessible target on gp120; 2G12 binds to oligosaccharides atthe tip of gp120; b12 interacts with the CD4 binding site; 2F5 and 4E10bind adjacent linear epitopes in the gp41 MPER.

FIG. 2 depicts vesicular stomatitis virus. The negative-sense RNA genome(schematically depicted at the top) encodes five genes in the order3′-N-P-M-G-L-5′. The surface of the virus particle (bottom) is decoratedwith approximately 1,200 copies of the glycoprotein (G), which isarranged as trimers. The matrix protein (M) lines the inner surface ofthe virus particle between the membrane and the nucleocapsid, probablymaking contact with G as well as the nucleocapsid (N) protein and givingthe virus particles their characteristic rod- or bullet-shapedmorphology. The polymerase (L) and phosphoprotein (P) are subunits ofthe RNA-dependent RNA polymerase complex.

FIG. 3 depicts the VSV glycoprotein. The model on the left side is thesoluble G ectodomain solved by Roche et al (Roche et al., Science 2007315, 843-848), which is composed of a number of structural elementsincluding an elongated β-sheet that contains the fusion peptide. In themiddle portion of the Figure, a graphic approximation (in pink) of aminoacid residues not included in the crystal structure was inserted, whichincludes the cytoplasmic tail (CT), the transmembrane (TM) domain, andthe short membrane-proximal ectodomain (Stem). Three epitope insertionpoints were used for preliminary studies: an a-helix at the tip (T), aloop (L) on the side, and a region in the Stem (S). The Stem, togetherwith the TM and CT domains, but without the remainder of the ectodomain,forms the G-Stem polypeptide, which is drawn at the right side of theFigure. The G-Stem protein can be incorporated into virions and can beused as a presentation platform for foreign epitopes.

FIG. 4 depicts HIV Env Immunogens presented on the VSV vector platform.The different chimeric envelope proteins are illustrated from top tobottom: i) the native VSV G trimer, ii) a G trimer with the gp41 MPERinserted into the stem region of G; iii) the G/Stem displaying MPERepitopes; and iv) the Env ectodomain including the MPER, which isincorporated into the VSV particle via the transmembrane segment andcytoplasmic tail of G.

FIG. 5 depicts insertion of the HIV gp41-derived 2F5 and/or 4E10 epitopeinto the ‘stem’ region of VSV G, which shares sequence similarities withthe gp41 MPER.

FIG. 6 depicts HIV-1 Env MPER and VSV G stem sequence alignment andinsertion/substitution strategies. Top, The MPER of HIV-1 gp41 (SEQ IDNO: 1) (JRFL strain) and the Stem region of VSV G (SEQ ID NO: 2)(Indiana strain) share sequence similarities, which guided the selectionof insertion or substitution points in the Stem region for the 2F5 and4E10 epitopes. The transmembrane domains and the first two residues ofthe cytoplasmic tails are depicted on the right. Hydrophobic residuesare shown in blue. Middle, Generation of the VSV G-2F5-Ins construct(SEQ ID NO: 5) by insertion of the 2F5 epitope (SEQ ID NO: 3) into the Gstem region (SEQ ID NO: 4). Flanking linker residues are shown in green.Bottom, Substitution of residues in the G stem region (SEQ ID NOS: 7 and10 respectively) with the 2F5 (SEQ ID NO: 6) and/or 4E10 (SEQ ID NO: 9)epitopes, resulting in the VSV G-2F5-Sub (SEQ ID NO: 8), VSV G-4E10-Sub(SEQ ID NO: 11), and VSV G-2F5-4E10-Sub (SEQ ID NO: 12) constructs.Sequences similarities between HIV gp41 and VSV G are shown in red.

FIG. 7 depicts insertion points for the 2F5 and 4E10 epitopes in thecontext of full-length VSV G. The leader peptide, ectodomain, Stem, TMand CT of VSV G are illustrated. The arrow denotes insertion of the 2F5epitope, while the orange and blue boxes indicate substitution of the2F5 and 4E10 epitopes, respectively.

FIG. 8 depicts the expression and antibody detection of the VSV Gconstructs. Western blot using VSV-G, 2F5 and 4E10 antibodies to detectthe G protein in lysates from 293T cells transfected with plasmidscoding for unmodified VSV G, VSV G-2F5-Ins, VSV G-2F5-Sub, VSVG-4E10-Sub, or VSV G-2F5-4E10-Sub. Mock denotes a transfection with an“empty” plasmid vector. The antibody used for detection is shown undereach panel. Molecular weight standards are indicated on the right ofeach gel.

FIG. 9 depicts the trimerization of the VSV G constructs. Western blotusing VSV-G antibody to detect oligomeric G protein on the surface of293T cells transfected with VSV G constructs, followed by incubationwith the chemical crosslinker3,3′-Dithiobis-[sulfosuccinimidylpropionate] (DTSSP) at variousconcentrations as indicated above each lane. Monomeric, dimeric andtrimeric VSV G forms are detected.

FIG. 10 depicts cell surface expression of VSV G constructs. 293T cellstransfected with VSV G constructs were stained with an antibody specificfor the ectodomain of VSV G, or with 2F5 or 4E10 antibodies, followed byanalysis of the samples by flow cytometry.

FIG. 11 depicts cell-cell fusion mediated by VSV G. 293T cellstransfected with VSV G constructs were exposed briefly to a medium withpH 5.2. After 6-8 hours, formation of syncitia was monitored using alight microscope. The inset in the panel for VSV G-2F5-4E10 at thebottom right shows a small syncitium, which occurs rarely for thisconstruct.

FIG. 12 depicts a reporter assay for functional analysis of modified VSVG proteins. A reporter lentivirus coding for green fluorescent protein(GFP) or luciferase (Luc) was packaged with Gag-Pol and pseudotyped withthe VSV G variants and subsequently used to infect naive 293T cells. GFPor luciferase expression was analyzed 72 hours post-infection.

FIG. 13 depicts infectivity of lentiviral particles pseudotyped with VSVG constructs. GFP reporter lentiviruses pseudotyped with VSV G variantswere generated in 293T cells and used subsequently to infect naive 293Tcells. GFP expression was monitored 72 hours post-infection.

FIG. 14 depicts quantification of infectivity of lentiviral particlespseudotyped with VSV G constructs. Naive 293T cells were infected withluciferase reporter lentiviruses pseudotyped with VSV G variants,followed by quantification of luciferase expression 48 hourspost-infection.

FIG. 15 depicts neutralization of lentiviral particles pseudotyped withVSV G constructs with the 2F5 or 4E10 antibodies. Luciferase reporterlentiviruses pseudotyped with VSV G, VSV G-2F5-Sub or VSV G-4E10-Subwere incubated with various concentrations of 2F5 (left panel) or 4E10antibody (right panel) prior to infection of naive cells. Luciferaseexpression was quantified 48 hours post-infection.

FIG. 16 depicts growth curves of recombinant VSV in Vero cells.Recombinant VSV (rVSV) containing the gene for wild-type G, G-2F5-Sub,G-4E10-Sub or G-2F5-4E10-Sub rescued in 293T cells was used to infectVero cells at a multiplicity of infection (m.o.i.) of 5. Aliquots of thesupernatant were taken at various times post-infection. Subsequently,naive Vero cells were infected with the samples, followed by a standardplaque assay to determine the viral titer for each time point.

FIG. 17 depicts neutralization of recombinant VSV with 2F5 and 4E10antibodies. Recombinant VSV containing wild-type G, G-2F5-Sub,G-4E10-Sub or G-2F5-4E10-Sub was incubated with various concentrationsof the broadly neutralizing monoclonal antibodies VI-10 (which reactswith the ectodomain of G), 2F5 or 4E10 before addition to naive Verocells. A standard plaque assay was used to determine the extent ofneutralization for each antibody and concentration.

FIGS. 18A and 18B depict a VSV G-Stem platform for expression of fusionproteins. A. Schematic illustration of the VSV genome, the G gene, andthe primary structures of the G and G-Stem proteins. B. Foreign genesequences are fused to the G-Stem via a Nhel restriction site, whichfacilitates incorporation of immunogen coding sequences.

FIGS. 19A-19C depict a schematic illustrating the membrane topology of Gand G-Stem proteins. A. Topology of the full-length G protein with theextracellular region, the stem, the transmembrane segment, and thecytoplasmic tail. Four different G-Stem constructs were generated: nostem, short stem, middle stem, and long stem. B. The gp41 MPER was fusedto the four G-Stem constructs (GS-MPER fusions). C. Amino acid sequenceof the G-Stem (SEQ ID NO: 13). The starting position for each GS variant(no, short, medium, long) is shown. The N-terminal signal sequence isshown in purple, whereas the transmembrane segment is colored red.

FIG. 20 depicts VSV Vector Design. The gene encoding G-Stem variants wasinserted into the VSV genome upstream of the N protein near the 3′ end.In addition, the full-length G protein is present in the genome. Uponexpression, both the G-Stem and full-length G will be incorporated intovirus particles as illustrated below the vector genome map.

FIGS. 21A-21D depict analysis of G-Stem-MPER Expression. A. Western Blotanalysis of rVSV containing the G-Stem-MPER variants (rVSV-GS-MPER) fromthe supernatant of infected cells using an anti-VSV-G antibody thatreacts with the cyoplasmic tail. LS, long stem; MS, medium stem; SS,short stem; NS, no stem. B. Western Blot analysis of rVSV-GS-MPER frominfected cells using an anti-VSV-G antibody. C. Western Blot analysis ofrVSV-GS-MPER with the 2F5 antibody. D. Western Blot analysis ofrVSV-GS-MPER with the 4E10 antibody.

FIG. 22 depicts various VSV G-HIV Env chimeras. The VSV glycoprotein Gis shown at the top with features labeled including the signal peptide(SP), the soluble extracellular domain, the Stem, transmembrane (TM)segment and cytoplasmic tail (CT). The HIV-1 Envelope (Env) protein,illustrated below G, is proteolytically processed into the extracellulargp120 and the gp41 domains, the latter containing the MPER, TM segmentand CT domains. Various chimeric EnvG proteins are shown at the bottom.Transition points between HIV gp41 and VSV G are be located i) beforethe CT, ii) before the TM domain, iii) before the MPER, or iv)N-terminal to the complete VSV G-Stem. Translocation of the protein intothe lumen of the endoplasmic reticulum can be driven by either the Envor the G signal peptide, although the efficiency and destination varywith the two signals. The ruler at the top denotes the number of aminoacid residues.

FIG. 23 depicts infectivity of rVSV-EnvG. a, Uninfected GHOST cells(expressing the HIV co-receptors CD4 and CCR5; Cecilia D., et al J.Virol. 1998 September; 7:6988-96) near full confluency. b, GHOST cellsinfected with rVSV-EnvG virus at 48 hours post-infection. The cytopathiceffect (CPE) is clearly visible.

FIG. 24 depicts evolution of Env or EnvG proteins expressed byrecombinant VSV. Recombinant VSV encoding a chimeric EnvG molecule aresubjected to serial passage and selective pressure. Virus particles thatbind with high avidity to 2F5 antibody, for example, are isolated afterstringent washing of the antibody beads. Infectious nucleocapsid isliberated from the antibody beads and transfected into CD4/CCR5-positivecells, which initiates a new round of infection. The new generation ofrecombinant virus undergoes further rounds of selection with increasedstringency, which enrich new variants of recombinant viruses that mayhave improved immunogenic properties.

FIG. 25 depicts rabbit immunogenicity testing. Vaccination and bloodcollection schedules are listed along a timeline (M, months; W, weeks)at the top. Analysis of antibody reactivity is illustrated in the flowdiagram at the left side. The chart on the right side outlines a typicalrabbit study.

FIG. 26 depicts a plan for vaccination, sampling, and SHIV Challenge.rVSV vaccine candidates are administered 3 times at 6-week intervalsafter which IV SHIV162P3 challenge is conducted using a challenge stockobtained from the NIH AIDS Research & Reference Reagent Program.

FIGS. 27A-27B depicts the plasmid sequence of pCINeo-VSV-G (SEQ ID NO:14) that encodes the G protein from the vesicular stomatitis Indianavirus. Applicants have optimized the gene sequence.

FIGS. 28A-28B depicts the unique XhoI and NotI sites (highlighted) addedto the 5′ and 3′ termini respectively of the VSV G coding sequence (SEQID NO: 15) as per the Optimization Strategy detailed in Example 5.

DETAILED DESCRIPTION

The terms “protein”, “peptide”, “polypeptide”, and “amino acid sequence”are used interchangeably herein to refer to polymers of amino acidresidues of any length. The polymer may be linear or branched, it maycomprise modified amino acids or amino acid analogs, and it may beinterrupted by chemical moieties other than amino acids. The terms alsoencompass an amino acid polymer that has been modified naturally or byintervention; for example disulfide bond formation, glycosylation,lipidation, acetylation, phosphorylation, or any other manipulation ormodification, such as conjugation with a labeling or bioactivecomponent.

As used herein, the terms “antigen” or “immunogen” are usedinterchangeably to refer to a substance, typically a protein, which iscapable of inducing an immune response in a subject. The term alsorefers to proteins that are immunologically active in the sense thatonce administered to a subject (either directly or by administering tothe subject a nucleotide sequence or vector that encodes the protein) isable to evoke an immune response of the humoral and/or cellular typedirected against that protein.

The term “antibody” includes intact molecules as well as fragmentsthereof, such as Fab, F(ab′)₂, Fv and scFv which are capable of bindingthe epitope determinant. These antibody fragments retain some ability toselectively bind with its antigen or receptor and include, for example:

-   -   (i) Fab, the fragment which contains a monovalent        antigen-binding fragment of an antibody molecule can be produced        by digestion of whole antibody with the enzyme papain to yield        an intact light chain and a portion of one heavy chain;    -   (ii) Fab′, the fragment of an antibody molecule can be obtained        by treating whole antibody with pepsin, followed by reduction,        to yield an intact light chain and a portion of the 20 heavy        chain; two Fab′ fragments are obtained per antibody molecule;    -   (iii) F(ab′)₂, the fragment of the antibody that can be obtained        by treating whole antibody with the enzyme pepsin without        subsequent reduction; F(ab′)₂ is a dimer of two Fab′ fragments        held together by two disulfide bonds;    -   (iv) scFv, including a genetically engineered fragment        containing the variable region of a heavy and a light chain as a        fused single chain molecule.

General methods of making these fragments are known in the art. (See forexample, Harlow and Lane, Antibodies: A Laboratory Manual, Cold SpringHarbor Laboratory, New York (1988), which is incorporated herein byreference).

It should be understood that the proteins, including the antibodiesand/or antigens of the invention may differ from the exact sequencesillustrated and described herein. Thus, the invention contemplatesdeletions, additions and substitutions to the sequences shown, so longas the sequences function in accordance with the methods of theinvention. In this regard, particularly preferred substitutions willgenerally be conservative in nature, i.e., those substitutions that takeplace within a family of amino acids. For example, amino acids aregenerally divided into four families: (1) acidic-aspartate andglutamate; (2) basic-lysine, arginine, histidine; (3) non-polar-alanine,valine, leucine, isoleucine, proline, phenylalanine, methionine,tryptophan; and (4) uncharged polar-glycine, asparagine, glutamine,cysteine, serine threonine, tyrosine. Phenylalanine, tryptophan, andtyrosine are sometimes classified as aromatic amino acids. It isreasonably predictable that an isolated replacement of leucine withisoleucine or valine, or vice versa; an aspartate with a glutamate orvice versa; a threonine with a serine or vice versa; or a similarconservative replacement of an amino acid with a structurally relatedamino acid, will not have a major effect on the biological activity.Proteins having substantially the same amino acid sequence as thesequences illustrated and described but possessing minor amino acidsubstitutions that do not substantially affect the immunogenicity of theprotein are, therefore, within the scope of the invention.

As used herein the terms “nucleotide sequences” and “nucleic acidsequences” refer to deoxyribonucleic acid (DNA) or ribonucleic acid(RNA) sequences, including, without limitation, messenger RNA (mRNA),DNA/RNA hybrids, or synthetic nucleic acids. The nucleic acid can besingle-stranded, or partially or completely double-stranded (duplex).Duplex nucleic acids can be homoduplex or heteroduplex.

As used herein the term “transgene” may used to refer to “recombinant”nucleotide sequences that may be derived from any of the nucleotidesequences encoding the proteins of the present invention. The term“recombinant” means a nucleotide sequence that has been manipulated “byman” and which does not occur in nature, or is linked to anothernucleotide sequence or found in a different arrangement in nature. It isunderstood that manipulated “by man” means manipulated by someartificial means, including by use of machines, codon optimization,restriction enzymes, etc.

For example, in one embodiment the nucleotide sequences may be mutatedsuch that the activity of the encoded proteins in vivo is abrogated. Inanother embodiment the nucleotide sequences may be codon optimized, forexample the codons may be optimized for human use. In preferredembodiments the nucleotide sequences of the invention are both mutatedto abrogate the normal in vivo function of the encoded proteins, andcodon optimized for human use. For example, each of the Gag, Pol, Env,Nef, RT, and Int sequences of the invention may be altered in theseways.

As regards codon optimization, the nucleic acid molecules of theinvention have a nucleotide sequence that encodes the antigens of theinvention and can be designed to employ codons that are used in thegenes of the subject in which the antigen is to be produced. Manyviruses, including HIV and other lentiviruses, use a large number ofrare codons and, by altering these codons to correspond to codonscommonly used in the desired subject, enhanced expression of theantigens can be achieved. In a preferred embodiment, the codons used are“humanized” codons, i.e., the codons are those that appear frequently inhighly expressed human genes (Andre et al., J. Virol. 72:1497-1503,1998) instead of those codons that are frequently used by HIV. Suchcodon usage provides for efficient expression of the transgenic HIVproteins in human cells. Any suitable method of codon optimization maybe used. Such methods, and the selection of such methods, are well knownto those of skill in the art. In addition, there are several companiesthat will optimize codons of sequences, such as Geneart (geneart.com).Thus, the nucleotide sequences of the invention can readily be codonoptimized.

The invention further encompasses nucleotide sequences encodingfunctionally and/or antigenically equivalent variants and derivatives ofthe antigens of the invention and functionally equivalent fragmentsthereof. These functionally equivalent variants, derivatives, andfragments display the ability to retain antigenic activity. Forinstance, changes in a DNA sequence that do not change the encoded aminoacid sequence, as well as those that result in conservativesubstitutions of amino acid residues, one or a few amino acid deletionsor additions, and substitution of amino acid residues by amino acidanalogs are those which will not significantly affect properties of theencoded polypeptide. Conservative amino acid substitutions areglycine/alanine; valine/isoleucine/leucine; asparagine/glutamine;aspartic acid/glutamic acid; serine/threonine/methionine;lysine/arginine; and phenylalanine/tyrosine/tryptophan. In oneembodiment, the variants have at least 50%, at least 55%, at least 60%,at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, atleast 86%, at least 87%, at least 88%, at least 89%, at least 90%, atleast 91%, at least 92%, at least 93%, at least 94%, at least 95%, atleast 96%, at least 97%, at least 98% or at least 99% homology oridentity to the antigen, epitope, immunogen, peptide or polypeptide ofinterest.

For the purposes of the present invention, sequence identity or homologyis determined by comparing the sequences when aligned so as to maximizeoverlap and identity while minimizing sequence gaps. In particular,sequence identity may be determined using any of a number ofmathematical algorithms. A nonlimiting example of a mathematicalalgorithm used for comparison of two sequences is the algorithm ofKarlin & Altschul, Proc. Natl. Acad. Sci. USA 1990; 87: 2264-2268,modified as in Karlin & Altschul, Proc. Natl. Acad. Sci. USA 1993;90:5873-5877.

Another example of a mathematical algorithm used for comparison ofsequences is the algorithm of Myers & Miller, CABIOS 1988; 4: 11-17.Such an algorithm is incorporated into the ALIGN program (version 2.0)which is part of the GCG sequence alignment software package. Whenutilizing the ALIGN program for comparing amino acid sequences, a PAM120weight residue table, a gap length penalty of 12, and a gap penalty of 4can be used. Yet another useful algorithm for identifying regions oflocal sequence similarity and alignment is the FASTA algorithm asdescribed in Pearson & Lipman, Proc. Natl. Acad. Sci. USA 1988; 85:2444-2448.

Advantageous for use according to the present invention is the WU-BLAST(Washington University BLAST) version 2.0 software. WU-BLAST version 2.0executable programs for several UNIX platforms can be downloaded fromftp://blast.wustl.edu/blast/executables. This program is based onWU-BLAST version 1.4, which in turn is based on the public domainNCBI-BLAST version 1.4 (Altschul & Gish, 1996, Local alignmentstatistics, Doolittle ed., Methods in Enzymology 266: 460-480; Altschulet al., Journal of Molecular Biology 1990; 215: 403-410; Gish & States,1993; Nature Genetics 3: 266-272; Karlin & Altschul, 1993; Proc. Natl.Acad. Sci. USA 90: 5873-5877; all of which are incorporated by referenceherein).

The various recombinant nucleotide sequences and antibodies and/orantigens of the invention are made using standard recombinant DNA andcloning techniques. Such techniques are well known to those of skill inthe art. See for example, “Molecular Cloning: A Laboratory Manual”,second edition (Sambrook et al. 1989).

The nucleotide sequences of the present invention may be inserted into“vectors.” The term “vector” is widely used and understood by those ofskill in the art, and as used herein the term “vector” is usedconsistent with its meaning to those of skill in the art. For example,the term “vector” is commonly used by those skilled in the art to referto a vehicle that allows or facilitates the transfer of nucleic acidmolecules from one environment to another or that allows or facilitatesthe manipulation of a nucleic acid molecule.

Any vector that allows expression of the antibodies and/or antigens ofthe present invention may be used in accordance with the presentinvention. In certain embodiments, the antigens and/or antibodies of thepresent invention may be used in vitro (such as using cell-freeexpression systems) and/or in cultured cells grown in vitro in order toproduce the encoded HIV-antigens and/or antibodies which may then beused for various applications such as in the production of proteinaceousvaccines. For such applications, any vector that allows expression ofthe antigens and/or antibodies in vitro and/or in cultured cells may beused.

For applications where it is desired that the antibodies and/or antigensbe expressed in vivo, for example when the transgenes of the inventionare used in DNA or DNA-containing vaccines, any vector that allows forthe expression of the antibodies and/or antigens of the presentinvention and is safe for use in vivo may be used. In preferredembodiments the vectors used are safe for use in humans, mammals and/orlaboratory animals.

For the antibodies and/or antigens of the present invention to beexpressed, the protein coding sequence should be “operably linked” toregulatory or nucleic acid control sequences that direct transcriptionand translation of the protein. As used herein, a coding sequence and anucleic acid control sequence or promoter are said to be “operablylinked” when they are covalently linked in such a way as to place theexpression or transcription and/or translation of the coding sequenceunder the influence or control of the nucleic acid control sequence. The“nucleic acid control sequence” can be any nucleic acid element, suchas, but not limited to promoters, enhancers, IRES, introns, and otherelements described herein that direct the expression of a nucleic acidsequence or coding sequence that is operably linked thereto. The term“promoter” will be used herein to refer to a group of transcriptionalcontrol modules that are clustered around the initiation site for RNApolymerase II and that when operationally linked to the protein codingsequences of the invention lead to the expression of the encodedprotein. The expression of the transgenes of the present invention canbe under the control of a constitutive promoter or of an induciblepromoter, which initiates transcription only when exposed to someparticular external stimulus, such as, without limitation, antibioticssuch as tetracycline, hormones such as ecdysone, or heavy metals. Thepromoter can also be specific to a particular cell-type, tissue ororgan. Many suitable promoters and enhancers are known in the art, andany such suitable promoter or enhancer may be used for expression of thetransgenes of the invention. For example, suitable promoters and/orenhancers can be selected from the Eukaryotic Promoter Database (EPDB).

The present invention relates to a recombinant vesicular stomatitisvirus (VSV) vector expressing a foreign epitope. Advantageously, theepitope is an HIV epitope. Any HIV epitope may be expressed in a VSVvector. Advantageously, the HIV epitope is an HIV antigen, HIV epitopeor an HIV immunogen, such as, but not limited to, the HIV antigens, HIVepitopes or HIV immunogens of U.S. Pat. Nos. 7,341,731; 7,335,364;7,329,807; 7,323,553; 7,320,859; 7,311,920; 7,306,798; 7,285,646;7,285,289; 7,285,271; 7,282,364; 7,273,695; 7,270,997; 7,262,270;7,244,819; 7,244,575; 7,232,567; 7,232,566; 7,223,844; 7,223,739;7,223,534; 7,223,368; 7,220,554; 7,214,530; 7,211,659; 7,211,432;7,205,159; 7,198,934; 7,195,768; 7,192,555; 7,189,826; 7,189,522;7,186,507; 7,179,645; 7,175,843; 7,172,761; 7,169,550; 7,157,083;7,153,509; 7,147,862; 7,141,550; 7,129,219; 7,122,188; 7,118,859;7,118,855; 7,118,751; 7,118,742; 7,105,655; 7,101,552; 7,097,9717,097,842; 7,094,405; 7,091,049; 7,090,648; 7,087,377; 7,083,787;7,070,787; 7,070,781; 7,060,273; 7,056,521; 7,056,519; 7,049,136;7,048,929; 7,033,593; 7,030,094; 7,022,326; 7,009,037; 7,008,622;7,001,759; 6,997,863; 6,995,008; 6,979,535; 6,974,574; 6,972,126;6,969,609; 6,964,769; 6,964,762; 6,958,158; 6,956,059; 6,953,689;6,951,648; 6,946,075; 6,927,031; 6,919,319; 6,919,318; 6,919,077;6,913,752; 6,911,315; 6,908,617; 6,908,612; 6,902,743; 6,900,010;6,893,869; 6,884,785; 6,884,435; 6,875,435; 6,867,005; 6,861,234;6,855,539; 6,841,381 6,841,345; 6,838,477; 6,821,955; 6,818,392;6,818,222; 6,815,217; 6,815,201; 6,812,026; 6,812,025; 6,812,024;6,808,923; 6,806,055; 6,803,231; 6,800,613; 6,800,288; 6,797,811;6,780,967; 6,780,598; 6,773,920; 6,764,682; 6,761,893; 6,753,015;6,750,005; 6,737,239; 6,737,067; 6,730,304; 6,720,310; 6,716,823;6,713,301; 6,713,070; 6,706,859; 6,699,722; 6,699,656; 6,696,291;6,692,745; 6,670,181; 6,670,115; 6,664,406; 6,657,055; 6,657,050;6,656,471; 6,653,066; 6,649,409; 6,649,372; 6,645,732; 6,641,816;6,635,469; 6,613,530; 6,605,427; 6,602,709 6,602,705; 6,600,023;6,596,477; 6,596,172; 6,593,103; 6,593,079; 6,579,673; 6,576,758;6,573,245; 6,573,040; 6,569,418; 6,569,340; 6,562,800; 6,558,961;6,551,828; 6,551,824; 6,548,275; 6,544,780; 6,544,752; 6,544,728;6,534,482; 6,534,312; 6,534,064; 6,531,572; 6,531,313; 6,525,179;6,525,028; 6,524,582; 6,521,449; 6,518,030; 6,518,015; 6,514,691;6,514,503; 6,511,845; 6,511,812; 6,511,801; 6,509,313; 6,506,384;6,503,882; 6,495,676; 6,495,526; 6,495,347; 6,492,123; 6,489,131;6,489,129; 6,482,614; 6,479,286; 6,479,284; 6,465,634; 6,461,6156,458,560; 6,458,527; 6,458,370; 6,451,601; 6,451,592; 6,451,323;6,436,407; 6,432,633; 6,428,970; 6,428,952; 6,428,790; 6,420,139;6,416,997; 6,410,318; 6,410,028; 6,410,014; 6,407,221; 6,406,710;6,403,092; 6,399,295; 6,392,013; 6,391,657; 6,384,198; 6,380,170;6,376,170; 6,372,426; 6,365,187; 6,358,739; 6,355,248; 6,355,247;6,348,450; 6,342,372; 6,342,228; 6,338,952; 6,337,179; 6,335,183;6,335,017; 6,331,404; 6,329,202; 6,329,173; 6,328,976; 6,322,964;6,319,666; 6,319,665; 6,319,500; 6,319,494; 6,316,205; 6,316,003;6,309,633; 6,306,625 6,296,807; 6,294,322; 6,291,239; 6,291,157;6,287,568; 6,284,456; 6,284,194; 6,274,337; 6,270,956; 6,270,769;6,268,484; 6,265,562; 6,265,149; 6,262,029; 6,261,762; 6,261,571;6,261,569; 6,258,599; 6,258,358; 6,248,332; 6,245,331; 6,242,461;6,241,986; 6,235,526; 6,235,466; 6,232,120; 6,228,361; 6,221,579;6,214,862; 6,214,804; 6,210,963; 6,210,873; 6,207,185; 6,203,974;6,197,755; 6,197,531; 6,197,496; 6,194,142; 6,190,871; 6,190,666;6,168,923; 6,156,302; 6,153,408; 6,153,393; 6,153,392; 6,153,378;6,153,377; 6,146,635; 6,146,614; 6,143,876 6,140,059; 6,140,043;6,139,746; 6,132,992; 6,124,306; 6,124,132; 6,121,006; 6,120,990;6,114,507; 6,114,143; 6,110,466; 6,107,020; 6,103,521; 6,100,234;6,099,848; 6,099,847; 6,096,291; 6,093,405; 6,090,392; 6,087,476;6,083,903; 6,080,846; 6,080,725; 6,074,650; 6,074,646; 6,070,126;6,063,905; 6,063,564; 6,060,256; 6,060,064; 6,048,530; 6,045,788;6,043,347; 6,043,248; 6,042,831; 6,037,165; 6,033,672; 6,030,772;6,030,770; 6,030,618; 6,025,141; 6,025,125; 6,020,468; 6,019,979;6,017,543; 6,017,537; 6,015,694; 6,015,661; 6,013,484; 6,013,4326,007,838; 6,004,811; 6,004,807; 6,004,763; 5,998,132; 5,993,819;5,989,806; 5,985,926; 5,985,641; 5,985,545; 5,981,537; 5,981,505;5,981,170; 5,976,551; 5,972,339; 5,965,371; 5,962,428; 5,962,318;5,961,979; 5,961,970; 5,958,765; 5,958,422; 5,955,647; 5,955,342;5,951,986; 5,951,975; 5,942,237; 5,939,277; 5,939,074; 5,935,580;5,928,930; 5,928,913; 5,928,644; 5,928,642; 5,925,513; 5,922,550;5,922,325; 5,919,458; 5,916,806; 5,916,563; 5,914,395; 5,914,109;5,912,338; 5,912,176; 5,912,170; 5,906,936; 5,895,650; 5,891,623;5,888,726; 5,885,580 5,885,578; 5,879,685; 5,876,731; 5,876,716;5,874,226; 5,872,012; 5,871,747; 5,869,058; 5,866,694; 5,866,341;5,866,320; 5,866,319; 5,866,137; 5,861,290; 5,858,740; 5,858,647;5,858,646; 5,858,369; 5,858,368; 5,858,366; 5,856,185; 5,854,400;5,853,736; 5,853,725; 5,853,724; 5,852,186; 5,851,829; 5,851,529;5,849,475; 5,849,288; 5,843,728; 5,843,723; 5,843,640; 5,843,635;5,840,480; 5,837,510; 5,837,250; 5,837,242; 5,834,599; 5,834,441;5,834,429; 5,834,256; 5,830,876; 5,830,641; 5,830,475; 5,830,458;5,830,457; 5,827,749; 5,827,723; 5,824,497 5,824,304; 5,821,047;5,817,767; 5,817,754; 5,817,637; 5,817,470; 5,817,318; 5,814,482;5,807,707; 5,804,604; 5,804,371; 5,800,822; 5,795,955; 5,795,743;5,795,572; 5,789,388; 5,780,279; 5,780,038; 5,776,703; 5,773,260;5,770,572; 5,766,844; 5,766,842; 5,766,625; 5,763,574; 5,763,190;5,762,965; 5,759,769; 5,756,666; 5,753,258; 5,750,373; 5,747,641;5,747,526; 5,747,028; 5,736,320; 5,736,146; 5,733,760; 5,731,189;5,728,385; 5,721,095; 5,716,826; 5,716,637; 5,716,613; 5,714,374;5,709,879; 5,709,860; 5,709,843; 5,705,331; 5,703,057; 5,702,7075,698,178; 5,688,914; 5,686,078; 5,681,831; 5,679,784; 5,674,984;5,672,472; 5,667,964; 5,667,783; 5,665,536; 5,665,355; 5,660,990;5,658,745; 5,658,569; 5,643,756; 5,641,624; 5,639,854; 5,639,598;5,637,677; 5,637,455; 5,633,234; 5,629,153; 5,627,025; 5,622,705;5,614,413; 5,610,035; 5,607,831; 5,606,026; 5,601,819; 5,597,688;5,593,972; 5,591,829; 5,591,823; 5,589,466; 5,587,285; 5,585,254;5,585,250; 5,580,773; 5,580,739; 5,580,563; 5,573,916; 5,571,667;5,569,468; 5,558,865; 5,556,745; 5,550,052; 5,543,328; 5,541,100;5,541,057; 5,534,406 5,529,765; 5,523,232; 5,516,895; 5,514,541;5,510,264; 5,500,161; 5,480,967; 5,480,966; 5,470,701; 5,468,606;5,462,852; 5,459,127; 5,449,601; 5,447,838; 5,447,837; 5,439,809;5,439,792; 5,418,136; 5,399,501; 5,397,695; 5,391,479; 5,384,240;5,374,519; 5,374,518; 5,374,516; 5,364,933; 5,359,046; 5,356,772;5,354,654; 5,344,755; 5,335,673; 5,332,567; 5,320,940; 5,317,009;5,312,902; 5,304,466; 5,296,347; 5,286,852, 5,268,265; 5,264,356;5,264,342; 5,260,308; 5,256,767; 5,256,561; 5,252,556; 5,230,998;5,230,887; 5,227,159; 5,225,347; 5,221,610, 5,217,861; 5,208,321;5,206,136; 5,198,346; 5,185,147; 5,178,865; 5,173,400; 5,173,399;5,166,050; 5,156,951, 5,135,864; 5,122,446; 5,120,662; 5,103,836;5,100,777; 5,100,662; 5,093,230; 5,077,284; 5,070,010; 5,068,174;5,066,782; 5,055,391; 5,043,262; 5,039,604; 5,039,522; 5,030,718;5,030,555; 5,030,449; 5,019,387; 5,013,556; 5,008,183; 5,004,697;4,997,772; 4,983,529; 4,983,387; 4,965,069; 4,945,082; 4,921,787;4,918,166; 4,900,548; 4,888,290; 4,886,742; 4,885,235; 4,870,003;4,869,903; 4,861,707; 4,853,326; 4,839,288; 4,833,072 and 4,795,739.

Advantageously, the HIV epitope may be an Env precursor or gp160epitope. The Env precursor or gp160 epitope may be recognized byantibodies PG9, PG16, 2G12, b12, 15 2F5, 4E10, Z13, or other broadpotent neutralizing antibodies.

In another embodiment, HIV, or immunogenic fragments thereof, may beutilized as the HIV epitope. For example, the HIV nucleotides of U.S.Pat. Nos. 7,393,949, 7,374,877, 7,306,901, 7,303,754, 7,173,014,7,122,180, 7,078,516, 7,022,814, 6,974,866, 6,958,211, 6,949,337,6,946,254, 6,896,900, 6,887,977, 6,870,045, 6,803,187, 6,794,129,6,773,915, 6,768,004, 6,706,268, 6,696,291, 6,692,955, 6,656,706,6,649,409, 6,627,442, 6,610,476, 6,602,705, 6,582,920, 6,557,296,6,531,587, 6,531,137, 6,500,623, 6,448,078, 6,429,306, 6,420,545,6,410,013, 6,407,077, 6,395,891, 6,355,789, 6,335,158, 6,323,185,6,316,183, 6,303,293, 6,300,056, 6,277,561, 6,270,975, 6,261,564,6,225,045, 6,222,024, 6,194,391, 6,194,142, 6,162,631, 6,114,167,6,114,109, 6,090,392, 6,060,587, 6,057,102, 6,054,565, 6,043,081,6,037,165, 6,034,233, 6,033,902, 6,030,769, 6,020,123, 6,015,661,6,010,895, 6,001,555, 5,985,661, 5,980,900, 5,972,596, 5,939,538,5,912,338, 5,869,339, 5,866,701, 5,866,694, 5,866,320, 5,866,137,5,864,027, 5,861,242, 5,858,785, 5,858,651, 5,849,475, 5,843,638,5,840,480, 5,821,046, 5,801,056, 5,786,177, 5,786,145, 5,773,247,5,770,703, 5,756,674, 5,741,706, 5,705,612, 5,693,752, 5,688,637,5,688,511, 5,684,147, 5,665,577, 5,585,263, 5,578,715, 5,571,712,5,567,603, 5,554,528, 5,545,726, 5,527,895, 5,527,894, 5,223,423,5,204,259, 5,144,019, 5,051,496 and 4,942,122 are useful for the presentinvention.

Any epitope recognized by an HIV antibody may be used in the presentinvention. For example, the anti-HIV antibodies of U.S. Pat. Nos.6,949,337, 6,900,010, 6,821,744, 6,768,004, 6,613,743, 6,534,312,6,511,830, 6,489,131, 6,242,197, 6,114,143, 6,074,646, 6,063,564,6,060,254, 5,919,457, 5,916,806, 5,871,732, 5,824,304, 5,773,247,5,736,320, 5,637,455, 5,587,285, 5,514,541, 5,317,009, 4,983,529,4,886,742, 4,870,003 and 4,795,739 are useful for the present invention.Furthermore, monoclonal anti-HIV antibodies of U.S. Pat. Nos. 7,074,556,7,074,554, 7,070,787, 7,060,273, 7,045,130, 7,033,593, RE39,057,7,008,622, 6,984,721, 6,972,126, 6,949,337, 6,946,465, 6,919,077,6,916,475, 6,911,315, 6,905,680, 6,900,010, 6,825,217, 6,824,975,6,818,392, 6,815,201, 6,812,026, 6,812,024, 6,797,811, 6,768,004,6,703,019, 6,689,118, 6,657,050, 6,608,179, 6,600,023, 6,596,497,6,589,748, 6,569,143, 6,548,275, 6,525,179, 6,524,582, 6,506,384,6,498,006, 6,489,131, 6,465,173, 6,461,612, 6,458,933, 6,432,633,6,410,318, 6,406,701, 6,395,275, 6,391,657, 6,391,635, 6,384,198,6,376,170, 6,372,217, 6,344,545, 6,337,181, 6,329,202, 6,319,665,6,319,500, 6,316,003, 6,312,931, 6,309,880, 6,296,807, 6,291,239,6,261,558, 6,248,514, 6,245,331, 6,242,197, 6,241,986, 6,228,361,6,221,580, 6,190,871, 6,177,253, 6,146,635, 6,146,627, 6,146,614,6,143,876, 6,132,992, 6,124,132, RE36,866, 6,114,143, 6,103,238,6,060,254, 6,039,684, 6,030,772, 6,020,468, 6,013,484, 6,008,044,5,998,132, 5,994,515, 5,993,812, 5,985,545, 5,981,278, 5,958,765,5,939,277, 5,928,930, 5,922,325, 5,919,457, 5,916,806, 5,914,109,5,911,989, 5,906,936, 5,889,158, 5,876,716, 5,874,226, 5,872,012,5,871,732, 5,866,694, 5,854,400, 5,849,583, 5,849,288, 5,840,480,5,840,305, 5,834,599, 5,831,034, 5,827,723, 5,821,047, 5,817,767,5,817,458, 5,804,440, 5,795,572, 5,783,670, 5,776,703, 5,773,225,5,766,944, 5,753,503, 5,750,373, 5,747,641, 5,736,341, 5,731,189,5,707,814, 5,702,707, 5,698,178, 5,695,927, 5,665,536, 5,658,745,5,652,138, 5,645,836, 5,635,345, 5,618,922, 5,610,035, 5,607,847,5,604,092, 5,601,819, 5,597,896, 5,597,688, 5,591,829, 5,558,865,5,514,541, 5,510,264, 5,478,753, 5,374,518, 5,374,516, 5,344,755,5,332,567, 5,300,433, 5,296,347, 5,286,852, 5,264,221, 5,260,308,5,256,561, 5,254,457, 5,230,998, 5,227,159, 5,223,408, 5,217,895,5,180,660, 5,173,399, 5,169,752, 5,166,050, 5,156,951, 5,140,105,5,135,864, 5,120,640, 5,108,904, 5,104,790, 5,049,389, 5,030,718,5,030,555, 5,004,697, 4,983,529, 4,888,290, 4,886,742 and 4,853,326, arealso useful for the present invention.

The vectors used in accordance with the present invention shouldtypically be chosen such that they contain a suitable gene regulatoryregion, such as a promoter or enhancer, such that the antigens and/orantibodies of the invention can be expressed.

For example, when the aim is to express the antibodies and/or antigensof the invention in vitro, or in cultured cells, or in any prokaryoticor eukaryotic system for the purpose of producing the protein(s) encodedby that antibody and/or antigen, then any suitable vector can be useddepending on the application. For example, plasmids, viral vectors,bacterial vectors, protozoal vectors, insect vectors, baculovirusexpression vectors, yeast vectors, mammalian cell vectors, and the like,can be used. Suitable vectors can be selected by the skilled artisantaking into consideration the characteristics of the vector and therequirements for expressing the antibodies and/or antigens under theidentified circumstances.

When the aim is to express the antibodies and/or antigens of theinvention in vivo in a subject, for example in order to generate animmune response against an HIV-1 antigen and/or protective immunityagainst HIV-1, expression vectors that are suitable for expression onthat subject, and that are safe for use in vivo, should be chosen. Forexample, in some embodiments it may be desired to express the antibodiesand/or antigens of the invention in a laboratory animal, such as forpre-clinical testing of the HIV-1 immunogenic compositions and vaccinesof the invention. In other embodiments, it will be desirable to expressthe antibodies and/or antigens of the invention in human subjects, suchas in clinical trials and for actual clinical use of the immunogeniccompositions and vaccine of the invention. Any vectors that are suitablefor such uses can be employed, and it is well within the capabilities ofthe skilled artisan to select a suitable vector. In some embodiments itmay be preferred that the vectors used for these in vivo applicationsare attenuated to vector from amplifying in the subject. For example, ifplasmid vectors are used, preferably they will lack an origin ofreplication that functions in the subject so as to enhance safety for invivo use in the subject. If viral vectors are used, preferably they areattenuated or replication-defective in the subject, again, so as toenhance safety for in vivo use in the subject.

In preferred embodiments of the present invention viral vectors areused. Viral expression vectors are well known to those skilled in theart and include, for example, viruses such as adenoviruses,adeno-associated viruses (AAV), alphaviruses, herpesviruses,retroviruses and poxviruses, including avipox viruses, attenuatedpoxviruses, vaccinia viruses, and particularly, the modified vacciniaAnkara virus (MVA; ATCC Accession No. VR-1566). Such viruses, when usedas expression vectors are innately non-pathogenic in the selectedsubjects such as humans or have been modified to render themnon-pathogenic in the selected subjects. For example,replication-defective adenoviruses and alphaviruses are well known andcan be used as gene delivery vectors.

The present invention relates to recombinant vesicular stomatitis (VSV)vectors, however, other vectors may be contemplated in other embodimentsof the invention such as, but not limited to, prime boost administrationcomprising administration of a recombinant VSV vector in combinationwith another recombinant vector expressing one or more HIV epitopes.

VSV is a very practical, safe, and immunogenic vector for conductinganimal studies, and an attractive candidate for developing vaccines foruse in humans. VSV is a member of the Rhabdoviridae family of envelopedviruses containing a nonsegmented, negative-sense RNA genome. The genomeis composed of 5 genes arranged sequentially 3′-N-P-M-G-L-5′, eachencoding a polypeptide found in mature virions. Notably, the surfaceglycoprotein G is a transmembrane polypeptide that is present in theviral envelope as a homotrimer, and like Env, it mediates cellattachment and infection.

In a first advantageous embodiment, the VSV G is replaced by HIV Env orfragments thereof. The latter will generate chimeric EnvG proteins (see,e.g. FIG. 22).

In a second advantageous embodiment, VSV G is a carrier or scaffoldadvantageously for Env MPER epitopes, however, VSV G as a carrier orscaffold may be extended to any foreign epitope (see, e.g., FIGS. 5-7).

In a third advantageous embodiment, Env MPER epitopes are fused to theVSV G-Stem molecule, however, any foreign epitope may be fused to theVSV G-Stem molecule (see, e.g, FIGS. 18-19).

In a fourth embodiment, the invention pertains to the evolutionarypotential of RNA viruses. Such viruses include but are not limited to:VSV, Measles virus, Canine distemper virus, Parainfluenza viruses,Sendai virus, Newcastle disease virus, Venezuelan equine encephalitisvirus, Sindbis virus, Semliki Forrest virus etc. Pertaining to theevolutionary potential of VSV, in the first step of EnvG construction, asmall panel of genes encoding different forms of EnvG molecules will beproduced to determine which motifs from G will optimize expression.Replication-competent ‘chimeric’ VSV-HIV viruses that lack the capacityto encode wild-type G and are dependent on EnvG for infection andpropagation, which are then utilized to direct the evolution of new EnvGmolecules that are expressed and incorporated into the virus withgreater efficiency.

In a fifth embodiment, the invention pertains to application ofselective pressure to enrich for molecules that are more immunogenic.The evolution process will occur primarily through nucleotidesubstitution, followed by selection using a broadly neutralizingantibody against HIV Env, e.g. 2F5 or 4E10, or a broad potent antibodyspecific for trimeric Env. Due to the nature of negative-strand virusreplication, base changes are far more frequent than deletions orinsertions, consequently the immunogen will evolve with amino acidsubstitutions. (see, e.g. FIG. 24)

The VSVs of U.S. Pat. Nos. 7,468,274; 7,419,829; 7,419,674; 7,344,838;7,332,316; 7,329,807; 7,323,337; 7,259,015; 7,244,818; 7,226,786;7,211,247; 7,202,079; 7,198,793; 7,198,784; 7,153,510; 7,070,994;6,969,598; 6,958,226; RE38,824; PP15,957; 6,890,735; 6,887,377;6,867,326; 6,867,036; 6,858,205; 6,835,568; 6,830,892; 6,818,209;6,790,641; 6,787,520; 6,743,620; 6,740,764; 6,740,635; 6,740,320;6,682,907; 6,673,784; 6,673,572; 6,669,936; 6,653,103; 6,607,912;6,558,923; 6,555,107; 6,533,855; 6,531,123; 6,506,604; 6,500,623;6,497,873; 6,489,142; 6,410,316; 6,410,313; 6,365,713; 6,348,312;6,326,487; 6,312,682; 6,303,331; 6,277,633; 6,207,455; 6,200,811;6,190,650; 6,171,862; 6,143,290; 6,133,027; 6,121,434; 6,103,462;6,069,134; 6,054,127; 6,034,073; 5,969,211; 5,935,822; 5,888,727;5,883,081; 5,876,727; 5,858,740; 5,843,723; 5,834,256; 5,817,491;5,792,604; 5,789,229; 5,773,003; 5,763,406; 5,760,184; 5,750,396;5,739,018; 5,698,446; 5,686,279; 5,670,354; 5,540,923; 5,512,421;5,090,194; 4,939,176; 4,738,846; 4,622,292; 4,556,556 and 4,396,628 maybe contemplated by the present invention.

The nucleotide sequences and vectors of the invention can be deliveredto cells, for example if aim is to express and the HIV-1 antigens incells in order to produce and isolate the expressed proteins, such asfrom cells grown in culture. For expressing the antibodies and/orantigens in cells any suitable transfection, transformation, or genedelivery methods can be used. Such methods are well known by thoseskilled in the art, and one of skill in the art would readily be able toselect a suitable method depending on the nature of the nucleotidesequences, vectors, and cell types used. For example, transfection,transformation, microinjection, infection, electroporation, lipofection,or liposome-mediated delivery could be used. Expression of theantibodies and/or antigens can be carried out in any suitable type ofhost cells, such as bacterial cells, yeast, insect cells, and mammaliancells. The antibodies and/or antigens of the invention can also beexpressed using including in vitro transcription/translation systems.All of such methods are well known by those skilled in the art, and oneof skill in the art would readily be able to select a suitable methoddepending on the nature of the nucleotide sequences, vectors, and celltypes used.

In preferred embodiments, the nucleotide sequences, antibodies and/orantigens of the invention are administered in vivo, for example wherethe aim is to produce an immunogenic response in a subject. A “subject”in the context of the present invention may be any animal. For example,in some embodiments it may be desired to express the transgenes of theinvention in a laboratory animal, such as for pre-clinical testing ofthe HIV-1 immunogenic compositions and vaccines of the invention. Inother embodiments, it will be desirable to express the antibodies and/orantigens of the invention in human subjects, such as in clinical trialsand for actual clinical use of the immunogenic compositions and vaccineof the invention. In preferred embodiments the subject is a human, forexample a human that is infected with, or is at risk of infection with,HIV-1.

For such in vivo applications the nucleotide sequences, antibodiesand/or antigens of the invention are preferably administered as acomponent of an immunogenic composition comprising the nucleotidesequences and/or antigens of the invention in admixture with apharmaceutically acceptable carrier. The immunogenic compositions of theinvention are useful to stimulate an immune response against HIV-1 andmay be used as one or more components of a prophylactic or therapeuticvaccine against HIV-1 for the prevention, amelioration or treatment ofAIDS. The nucleic acids and vectors of the invention are particularlyuseful for providing genetic vaccines, i.e. vaccines for delivering thenucleic acids encoding the antibodies and/or antigens of the inventionto a subject, such as a human, such that the antibodies and/or antigensare then expressed in the subject to elicit an immune response.

The compositions of the invention may be injectable suspensions,solutions, sprays, lyophilized powders, syrups, elixirs and the like.Any suitable form of composition may be used. To prepare such acomposition, a nucleic acid or vector of the invention, having thedesired degree of purity, is mixed with one or more pharmaceuticallyacceptable carriers and/or excipients. The carriers and excipients mustbe “acceptable” in the sense of being compatible with the otheringredients of the composition. Acceptable carriers, excipients, orstabilizers are nontoxic to recipients at the dosages and concentrationsemployed, and include, but are not limited to, water, saline, phosphatebuffered saline, dextrose, glycerol, ethanol, or combinations thereof,buffers such as phosphate, citrate, and other organic acids;antioxidants including ascorbic acid and methionine; preservatives (suchas octadecyldimethylbenzyl ammonium chloride; hexamethonium chloride;benzalkonium chloride, benzethonium chloride; phenol, butyl or benzylalcohol; alkyl parabens such as methyl or propyl paraben; catechol;resorcinol; cyclohexanol; 3-pentanol; and m-cresol); low molecularweight (less than about 10 residues) polypeptide; proteins, such asserum albumin, gelatin, or immunoglobulins; hydrophilic polymers such aspolyvinylpyrrolidone; amino acids such as glycine, glutamine,asparagine, histidine, arginine, or lysine; monosaccharides,disaccharides, and other carbohydrates including glucose, mannose, ordextrins; chelating agents such as EDTA; sugars such as sucrose,mannitol, trehalose or sorbitol; salt-forming counter-ions such assodium; metal complexes (e.g., Zn-protein complexes); and/or non-ionicsurfactants such as TWEEN™, PLURONICS™ or polyethylene glycol (PEG).

An immunogenic or immunological composition can also be formulated inthe form of an oil-in-water emulsion. The oil-in-water emulsion can bebased, for example, on light liquid paraffin oil (European Pharmacopeatype); isoprenoid oil such as squalane, squalene, EICOSANE™ ortetratetracontane; oil resulting from the oligomerization of alkene(s),e.g., isobutene or decene; esters of acids or of alcohols containing alinear alkyl group, such as plant oils, ethyl oleate, propylene glycoldi(caprylate/caprate), glyceryl tri(caprylate/caprate) or propyleneglycol dioleate; esters of branched fatty acids or alcohols, e.g.,isostearic acid esters. The oil advantageously is used in combinationwith emulsifiers to form the emulsion. The emulsifiers can be nonionicsurfactants, such as esters of sorbitan, mannide (e.g., anhydromannitololeate), glycerol, polyglycerol, propylene glycol, and oleic,isostearic, ricinoleic, or hydroxystearic acid, which are optionallyethoxylated, and polyoxypropylene-polyoxyethylene copolymer blocks, suchas the Pluronic® products, e.g., L121. The adjuvant can be a mixture ofemulsifier(s), micelle-forming agent, and oil such as that which iscommercially available under the name Provax® (DEC Pharmaceuticals, SanDiego, Calif.).

The immunogenic compositions of the invention can contain additionalsubstances, such as wetting or emulsifying agents, buffering agents, oradjuvants to enhance the effectiveness of the vaccines (Remington'sPharmaceutical Sciences, 18th edition, Mack Publishing Company, (ed.)1980).

Adjuvants may also be included. Adjuvants include, but are not limitedto, mineral salts (e.g., AlK(SO₄)₂, AlNa(SO₄)₂, AlNH(SO₄)₂, silica,alum, Al(OH)₃, Ca₃(PO₄)₂, kaolin, or carbon), polynucleotides with orwithout immune stimulating complexes (ISCOMs) (e.g., CpGoligonucleotides, such as those described in Chuang, T. H. et al, (2002)J. Leuk. Biol. 71(3): 538-44; Ahmad-Nejad, P. et al (2002) Eur. J.Immunol. 32(7): 1958-68; poly IC or poly AU acids, polyarginine with orwithout CpG (also known in the art as IC31; see Schellack, C. et al(2003) Proceedings of the 34th Annual Meeting of the German Society ofImmunology; Lingnau, K. et al (2002) Vaccine 20(29-30): 3498-508),JuvaVax™ (U.S. Pat. No. 6,693,086), certain natural substances (e.g.,wax D from Mycobacterium tuberculosis, substances found inCornyebacterium parvum, Bordetella pertussis, or members of the genusBrucella), flagellin (Toll-like receptor 5 ligand; see McSorley, S. J.et al (2002) J. Immunol. 169(7): 3914-9), saponins such as QS21, QS17,and QS7 (U.S. Pat. Nos. 5,057,540; 5,650,398; 6,524,584; 6,645,495),monophosphoryl lipid A, in particular, 3-de-O-acylated monophosphoryllipid A (3D-MPL), imiquimod (also known in the art as IQM andcommercially available as Aldara®; U.S. Pat. Nos. 4,689,338; 5,238,944;Zuber, A. K. et al (2004) 22(13-14): 1791-8), and the CCR5 inhibitorCMPD167 (see Veazey, R. S. et al (2003) J. Exp. Med. 198: 1551-1562).

Aluminum hydroxide or phosphate (alum) are commonly used at 0.05 to 0.1%solution in phosphate buffered saline. Other adjuvants that can be used,especially with DNA vaccines, are cholera toxin, especiallyCTA1-DD/ISCOMs (see Mowat, A. M. et al (2001) J. Immunol. 167(6):3398-405), polyphosphazenes (Allcock, H. R. (1998) App. OrganometallicChem. 12(10-11): 659-666; Payne, L. G. et al (1995) Pharm. Biotechnol.6: 473-93), cytokines such as, but not limited to, IL-2, IL-4, GM-CSF,IL-12, IL-15 IGF-1, IFN-α, IFN-β, and IFN-γ (Boyer et al., (2002) J.Liposome Res. 121:137-142; WO01/095919), immunoregulatory proteins suchas CD4OL (ADX40; see, for example, WO03/063899), and the CD1a ligand ofnatural killer cells (also known as CRONY or α-galactosyl ceramide; seeGreen, T. D. et al, (2003) J. Virol. 77(3): 2046-2055),immunostimulatory fusion proteins such as IL-2 fused to the Fc fragmentof immunoglobulins (Barouch et al., Science 290:486-492, 2000) andco-stimulatory molecules B7.1 and B7.2 (Boyer), all of which can beadministered either as proteins or in the form of DNA, on the sameexpression vectors as those encoding the antigens of the invention or onseparate expression vectors.

In an advantageous embodiment, the adjuvants may be lecithin is combinedwith an acrylic polymer (Adjuplex-LAP), lecithin coated oil droplets inan oil-in-water emulsion (Adjuplex-LE) or lecithin and acrylic polymerin an oil-in-water emulsion (Adjuplex-LAO) (Advanced BioAdjuvants(ABA)).

The immunogenic compositions can be designed to introduce the nucleicacids or expression vectors to a desired site of action and release itat an appropriate and controllable rate. Methods of preparingcontrolled-release formulations are known in the art. For example,controlled release preparations can be produced by the use of polymersto complex or absorb the immunogen and/or immunogenic composition. Acontrolled-release formulations can be prepared using appropriatemacromolecules (for example, polyesters, polyamino acids, polyvinyl,pyrrolidone, ethylenevinylacetate, methylcellulose,carboxymethylcellulose, or protamine sulfate) known to provide thedesired controlled release characteristics or release profile. Anotherpossible method to control the duration of action by acontrolled-release preparation is to incorporate the active ingredientsinto particles of a polymeric material such as, for example, polyesters,polyamino acids, hydrogels, polylactic acid, polyglycolic acid,copolymers of these acids, or ethylene vinylacetate copolymers.Alternatively, instead of incorporating these active ingredients intopolymeric particles, it is possible to entrap these materials intomicrocapsules prepared, for example, by coacervation techniques or byinterfacial polymerization, for example, hydroxymethylcellulose orgelatin-microcapsule and poly-(methylmethacrylate) microcapsule,respectively, in colloidal drug delivery systems (for example,liposomes, albumin microspheres, microemulsions, nano-particles andnanocapsules) or in macroemulsions. Such techniques are disclosed in NewTrends and Developments in Vaccines, Voller et al. (eds.), UniversityPark Press, Baltimore, Md., 1978 and Remington's PharmaceuticalSciences, 16th edition.

Suitable dosages of the nucleic acids and expression vectors of theinvention (collectively, the immunogens) in the immunogenic compositionof the invention can be readily determined by those of skill in the art.For example, the dosage of the immunogens can vary depending on theroute of administration and the size of the subject. Suitable doses canbe determined by those of skill in the art, for example by measuring theimmune response of a subject, such as a laboratry animal, usingconventional immunological techniques, and adjusting the dosages asappropriate. Such techniques for measuring the immune response of thesubject include but are not limited to, chromium release assays,tetramer binding assays, IFN-γ ELISPOT assays, IL-2 ELISPOT assays,intracellular cytokine assays, and other immunological detection assays,e.g., as detailed in the text “Antibodies: A Laboratory Manual” by EdHarlow and David Lane.

When provided prophylactically, the immunogenic compositions of theinvention are ideally administered to a subject in advance of HIVinfection, or evidence of HIV infection, or in advance of any symptomdue to AIDS, especially in high-risk subjects. The prophylacticadministration of the immunogenic compositions can serve to provideprotective immunity of a subject against HIV-1 infection or to preventor attenuate the progression of AIDS in a subject already infected withHIV-1. When provided therapeutically, the immunogenic compositions canserve to ameliorate and treat AIDS symptoms and are advantageously usedas soon after infection as possible, preferably before appearance of anysymptoms of AIDS but may also be used at (or after) the onset of thedisease symptoms.

The immunogenic compositions can be administered using any suitabledelivery method including, but not limited to, intramuscular,intravenous, intradermal, mucosal, and topical delivery. Such techniquesare well known to those of skill in the art. More specific examples ofdelivery methods are intramuscular injection, intradermal injection, andsubcutaneous injection. However, delivery need not be limited toinjection methods. Further, delivery of DNA to animal tissue has beenachieved by cationic liposomes (Watanabe et al., (1994) Mol. Reprod.Dev. 38:268-274; and WO 96/20013), direct injection of naked DNA intoanimal muscle tissue (Robinson et al., (1993) Vaccine 11:957-960;Hoffman et al., (1994) Vaccine 12: 1529-1533; Xiang et al., (1994)Virology 199: 132-140; Webster et al., (1994) Vaccine 12: 1495-1498;Davis et al., (1994) Vaccine 12: 1503-1509; and Davis et al., (1993)Hum. Mol. Gen. 2: 1847-1851), or intradermal injection of DNA using“gene gun” technology (Johnston et al., (1994) Meth. Cell Biol.43:353-365). Alternatively, delivery routes can be oral, intranasal orby any other suitable route. Delivery also be accomplished via a mucosalsurface such as the anal, vaginal or oral mucosa.

Immunization schedules (or regimens) are well known for animals(including humans) and can be readily determined for the particularsubject and immunogenic composition. Hence, the immunogens can beadministered one or more times to the subject. Preferably, there is aset time interval between separate administrations of the immunogeniccomposition. While this interval varies for every subject, typically itranges from 10 days to several weeks, and is often 2, 4, 6 or 8 weeks.For humans, the interval is typically from 2 to 6 weeks. Theimmunization regimes typically have from 1 to 6 administrations of theimmunogenic composition, but may have as few as one or two or four. Themethods of inducing an immune response can also include administrationof an adjuvant with the immunogens. In some instances, annual, biannualor other long interval (5-10 years) booster immunization can supplementthe initial immunization protocol.

The present methods also include a variety of prime-boost regimens, forexample DNA prime-Adenovirus boost regimens. In these methods, one ormore priming immunizations are followed by one or more boostingimmunizations. The actual immunogenic composition can be the same ordifferent for each immunization and the type of immunogenic composition(e.g., containing protein or expression vector), the route, andformulation of the immunogens can also be varied. For example, if anexpression vector is used for the priming and boosting steps, it caneither be of the same or different type (e.g., DNA or bacterial or viralexpression vector). One useful prime-boost regimen provides for twopriming immunizations, four weeks apart, followed by two boostingimmunizations at 4 and 8 weeks after the last priming immunization. Itshould also be readily apparent to one of skill in the art that thereare several permutations and combinations that are encompassed using theDNA, bacterial and viral expression vectors of the invention to providepriming and boosting regimens.

The prime-boost regimen can also include VSV vectors that derive their Gprotein or G/Stem protein from different serotype vesicular stomatitisviruses (Rose N F, Roberts A, Buonocore L, Rose J K. Glycoproteinexchange vectors based on vesicular stomatitis virus allow effectiveboosting and generation of neutralizing antibodies to a primary isolateof human immunodeficiency virus type 1. J Virol. 2000 December;74(23):10903-10). The VSV vectors used in these examples contain a G orG/Stem protein derived from the Indiana serotype of VSV. Vectors canalso be constructed to express epiotpes in the context of G or G/Stemmolecules derived from other VSV serotypes (i.e. vesicular stomatitisNew Jersey virus or vesicular stomatitis Alagoas virus) or othervesiculoviruses (i.e. Chandipura virus, Cocal virus, Isfahan virus).Thus an epitope like the HIV MPER can be delivered in a prime in thecontext of an G or G/Stem moelcule that is from the Indiana serotype andthe immune system can be boosted with a vector that expresses epitopesin the context of second serotype like New Jersey. This circumventsanti-G immunity elicited by the prime, and helps focus the boostresponse agains the foreign epitope.

A specific embodiment of the invention provides methods of inducing animmune response against HIV in a subject by administering an immunogeniccomposition of the invention, preferably comprising an adenovirus vectorcontaining DNA encoding one or more of the epitopes of the invention,one or more times to a subject wherein the epitopes are expressed at alevel sufficient to induce a specific immune response in the subject.Such immunizations can be repeated multiple times at time intervals ofat least 2, 4 or 6 weeks (or more) in accordance with a desiredimmunization regime.

The immunogenic compositions of the invention can be administered alone,or can be co-administered, or sequentially administered, with other HIVimmunogens and/or HIV immunogenic compositions, e.g., with “other”immunological, antigenic or vaccine or therapeutic compositions therebyproviding multivalent or “cocktail” or combination compositions of theinvention and methods of employing them. Again, the ingredients andmanner (sequential or co-administration) of administration, as well asdosages can be determined taking into consideration such factors as theage, sex, weight, species and condition of the particular subject, andthe route of administration.

When used in combination, the other HIV immunogens can be administeredat the same time or at different times as part of an overallimmunization regime, e.g., as part of a prime-boost regimen or otherimmunization protocol. In an advantageous embodiment, the other HIVimmunogen is env, preferably the HIV env trimer.

Many other HIV immunogens are known in the art, one such preferredimmunogen is HIVA (described in WO 01/47955), which can be administeredas a protein, on a plasmid (e.g., pTHr.HIVA) or in a viral vector (e.g.,MVA.HIVA). Another such HIV immunogen is RENTA (described inPCT/US2004/037699), which can also be administered as a protein, on aplasmid (e.g., pTHr.RENTA) or in a viral vector (e.g., MVA.RENTA).

For example, one method of inducing an immune response against HIV in ahuman subject comprises administering at least one priming dose of anHIV immunogen and at least one boosting dose of an HIV immunogen,wherein the immunogen in each dose can be the same or different,provided that at least one of the immunogens is an epitope of thepresent invention, a nucleic acid encoding an epitope of the inventionor an expression vector, preferably a VSV vector, encoding an epitope ofthe invention, and wherein the immunogens are administered in an amountor expressed at a level sufficient to induce an HIV-specific immuneresponse in the subject. The HIV-specific immune response can include anHIV-specific T-cell immune response or an HIV-specific B-cell immuneresponse. Such immunizations can be done at intervals, preferably of atleast 2-6 or more weeks.

It is to be understood and expected that variations in the principles ofinvention as described above may be made by one skilled in the art andit is intended that such modifications, changes, and substitutions areto be included within the scope of the present invention.

The invention will now be further described by way of the followingnon-limiting examples.

EXAMPLES Example 1 Insertion of the HIV-1 gp41 Epitopes 2F5 and 4E10into the Membrane Proximal Region of the Vesicular Stomatitis VirusGlycoprotein

The membrane-proximal external region (MPER) of HIV-1 gp41, which isrecognized by the broadly neutralizing monoclonal antibodies 2F5 and4E10, is an important target for an HIV vaccine. However, efforts tomimick the 2F5 and 4E10 epitopes outside the context 30 of the gp41 MPERhave had minimal success so far. In this study, Applicants used theenvelope glycoprotein G of Vesicular Stomatitis Virus (VSV) as ascaffold. VSV G, which forms homotrimeric spikes on the viral surface,is responsible for binding of the virus to cells and promotes fusion ofthe viral and cellular membranes. The “stem” region of VSV G, which liesimmediately N-terminal of its single transmembrane segment, sharessequence similarities with the gp41 MPER. Applicants inserted the gp41sequences corresponding to the 2F5 and 4E10 neutralizing epitopes intothe stem region of VSV G and evaluated the function and antibodyreactivity of the chimeric polypeptides. VSV-G-2F5 and VSV-G-4E10 formedtrimers and were transported to the cell surface, where they weredetected by the 2F5 and 4E10 monoclonal antibodies, respectively.Reporter lentiviruses pseudotyped with VSV G-2F5 or VSV-G-4E10 wereinfectious, and they were efficiently neutralized by the 2F5 or 4E10monoclonal antibodies. Recombinant VSV containing G-2F5, G-4E10 orG-2F5-4E10 on the viral surface was infectious, replication-competent,and sensitive to neutralization by the 2F5 or 4E10 monoclonalantibodies. Applicants are currently determining if the recombinant VSVsencoding MPER epitopes elicit neutralizing antibodies specific for theHIV gp41 epitopes in a small animal model. Taken together, Applicants'approach represents a novel strategy to develop a vaccine that induces ahumoral immune response against HIV.

Example 2 Using VSV Vectors to Display and Evolve Novel HIV EnvelopeImmunogens.

The goal of this Example is to design and develop novel HIV-1 envelopeprotein (Env) immunogens capable of eliciting broadly protectiveneutralizing antibody responses for use as vaccine candidates.Applicants take advantage of the unique biological properties ofvesicular stomatitis virus (VSV) as vaccine delivery vehicle to presentand effectively deliver HIV Env immunogens. In addition, Applicants usethe high evolutionary potential of VSV to biologically derive uniquemutant HIV Envs with enhanced immunogenicity. Novel candidates are usedto vaccinate rabbits to determine their capacity to elicit antibodieswith enhanced HIV neutralizing activity, and those VSV-vectored vaccinesthat evoke responses with increased breadth of neutralization are testedin macaques. Applicants achieve these goals by completing the SpecificAims below:

-   -   1. Vaccine Platform 1: Optimize HIV Env (derived from        SHIV_(SF162P3)) for expression as functional stable trimers on        the surface of VSV particles, and produce ‘chimeric viruses’, in        which the gene encoding the VSV surface glycoprotein (G) are        functionally replaced by HIV Env. Env modifications described        below are investigated to identify the optimal form for        expressing abundant functional trimers on VSV particles that        specifically direct infection of cells expressing the CD4 and        CCR5 coreceptors (CD4/CCR5⁺ cells). Additionally, Applicants        take advantage of the innate ability of VSV to rapidly accrue        adaptive mutations to further optimize expression of functional        Env trimers by subjecting replication-competent VSV-Env chimeric        viruses to serial passage on CD4/CCR5⁺ cell lines to        biologically select for Env mutations that improve replicative        fitness. Moreover, to develop additional novel Env immunogens,        methods to apply selective pressure during serial passage are        developed using the broadly neutralizing antibodies against Env        (e.g. monoclonal antibodies 2F5, 4E10, 2G12, b12, PG9, PG16 and        other antibodies, including broad potent neutralizing        trimer-specific antibodies).    -   2. Vaccine Platform 2: Produce recombinant VSV (rVSV) vectors        that encode modified forms of VSV G, which harbor epitopes from        the HIV Env membrane proximal external region (MPER). This takes        advantage of several G protein properties including: i) it is a        glycosylated transmembrane protein abundantly expressed on the        VSV particle; ii) it is a potent immunogen; iii) it contains a        hydrophobic membrane-proximal region that resembles the Env        MPER, and iv) G trimerizes and provides a platform for        multimeric configurations of MPER epitopes. Although several        domains in G are tested as sites for insertion of MPER        sequences, Applicants focus on the membrane proximal region of        G, which provides a similar membrane-associated environment for        the most authentic presentation of MPER epitopes. Env MPER        insertions that do not abolish the function of VSV G are        delivered using VSV vectors and advanced into rabbit        immunogenicity studies. Additionally, VSV encoding G-MPER        hybrids are subjected to serial passage to determine whether        virus expressing a fitness advantage emerges with unique        mutations that affect the MPER epitope configuration. Moreover,        serial passage also are conducted using conditions that select        virus expressing G-MPER proteins that bind with high avidity to        the 2F5 and 4E10 mAbs to derive unique immunogens.    -   3. Vaccine Platform 3: An N-terminally truncated form of VSV G        (called G/Stem) are used to present Env epitope sequences on the        surface of VSV particles. The G/Stem molecule contains the        cytoplasmic tail (CT) and trans-membrane (TM) spanning domains        of G as well as a short 16- to 68-amino acid membrane proximal        extracellular polypeptide (the Stem) to which HIV Env epitopes        are appended. Several forms of G/Stem, which vary in length and        amino acid sequence, are investigated to determine the optimal        form for display of MPER epitopes on the surface of VSV        particles and the plasma membrane of infected cells. VSV        encoding G/Stem fusion proteins can be propagated using G        trans-complementation or by generating recombinant virus that        contains a functional G gene in addition to the G/Stem coding        sequence. Novel G/Stem-MPER molecules are evolved by serial        passage under conditions that select for vectors encoding mutant        molecules that bind to the 2F5 and 4E10 mAbs with high affinity.    -   4. In Vivo Studies: After validating their in vitro properties,        promising vaccine candidates developed in Aims 1-3 are evaluated        by vaccinating rabbits. Enzyme-linked immunosorbent assays        (ELISAs) are conducted first to screen for serum antibodies that        react with HIV Env, and those immune sera that contain        significant titers are evaluated in HIV neutralization assays        using virus-like particles pseudotyped with Env from various HIV        strains. The top rVSV-Env vaccine candidates that evoke        production of broadly neutralizing antibodies in vaccinated        rabbits are advanced into nonhuman primate studies. Rhesus        macaques are vaccinated to determine whether immunization        protects macaques from subsequent intravenous challenge with the        SIV-HIV chimeric virus SHIV_(SF162P3), which expresses an HIV        envelope protein.

Example 3: Optimization of Immunogen Presentation by G-Stem Vectors

To develop a platform that can be used to display immunogens on thesurface of virus particles or infected cells, Applicants have engineeredvesicular stomatitis virus (VSV) vectors to encode a truncated form ofthe viral transmembrane glycoprotein protein (G) that can be modified toexpress foreign epitopes anchored to virus envelop or cell membrane. Thetruncated form of G, called G-Stem (FIG. 18A), retains amino acidsequences that are essential for directing insertion of the moleculeinto the membrane (the signal peptide), anchoring the protein in theviral envelop or cellular lipid bilayer (the transmembrane domain; TM),and promoting incorporation into the budding viral particle (C-terminaldomain). Additionally, a small membrane proximal region of the externaldomain of G (the Stem) is retained in most constructs because itprovides a short stalk on which to append epitopes (FIG. 18B), andimportantly, sequences in the Stem are known to promote efficientassembly of VSV particles [Robison & Whitt, J Virol 2000; 74:2239-2246].

Because the Stem domain plays at least two significant roles inApplicants' epitope display vectors—it serves as the platform on whichepitopes are attached and displayed, and it plays a role in VSVmaturation—Applicants anticipated that it might be necessary toempirically determine the optimal Stem sequence needed for expressionand membrane incorporation of G-Stem-Epitope fusion proteins. Applicantstested this assumption by constructing 4 different G-Stem fusionproteins that contained the HIV Env membrane proximal external region(MPER) [Montero et al., Microbiol Mol Biol Rev 2008; 72:54-84] fused toStem domains that were 68, 42, 16 or 0 amino acids in length, referredto as long stem (LS), medium stem (MS), short stem (SS), and no stem(NS), respectively (FIGS. 19A-C).

The 4 G-Stem-MPER (GS-MPER) molecules were expressed using a novelreplication-competent VSV vector that retains a functional G protein andexpresses the GS-MPER fusion proteins from an added transcription unitinserted in the highly-transcribed promoter proximal position in theviral genome (FIG. 20). Consequently, the MPER expression vectorsexpress GS-MPER fusion proteins as well as wild-type G protein.Expression of native G protein confers a replication-competent phenotypeof these recombinant viruses, and importantly, this also means thatinfected cells will produce wild-type G and GS-MPER proteins and thatboth proteins can be inserted into cell membrane and viral envelop(right side of FIG. 20B).

After the recombinant VSV-G-Stem-MPER vectors were constructed, theywere used to infect Vero cells and assess expression of the GS-MPERfusion proteins and determine their relative abundance in virusparticles (FIG. 21). FIG. 21 shows a Western blot that was used toanalyze G and G-Stem-MPER proteins found in the medium supernatant ofinfected cells. The source of G and GS MPER fusion proteins in thesupernatant primarily should be virus that has budded out of infectedcells; therefore, the proteins visualized in Panel A provide an estimateof the relative G and GS-MPER abundance in progeny virus particles. Theblot in Panel A was reacted with antibody that recognizes the C-terminusof VSV G, which is present on both the native G protein the G-Stem-MPERmolecules. The results indicate that NS-MPER and SS-MPER are present athigher levels in the virus particle than MS-MPER or LS-MPER, and thatnone of the G-Stem-MPERs are as abundant as the native G protein. It isimportant to note that a proteolytic fragment of G comigrates with theNS-MPER at the top of the gel (Lane 6) making it difficult to estimateits abundance. The relative amount of the 4 MPER-containing molecules ismore clearly shown in Panels C and D where the GS-MPER proteins arereacted with MPER-Specific monoclonal antibodies 2F5 and 4E10. In PanelC for example, the relative amounts of NS-MPER (Lane 6) and SS-MPER(Lane 5) are clearly greater than MS- and LS-MPER (Lanes 3 and 4) invirus particles found in the supernatant. It is worth noting that theLS-MPER molecule is expressed at relatively high levels in infectedcells as shown in Panel B (Lane 2) suggesting that this form ofG-Stem-MPER is expressed but not efficiently incorporated into virusparticles. The MS-MPER protein is evident in the infected cells (PanelB, Lane 3) but at low levels indicating that it is expressed poorly orit is unstable compared to the other GS-MPERS. Finally, it is notablethat the NS-MPER protein, which lacks the Stem completely, seems to beincorporated at the highest levels of all of the G-Stem-MPERs (FIGS. 21Cand D, Lanes 5 and 6). This finding seems to be contrary to the knownrole of Stem in virus particle maturation [Robison & Whitt, J Virol2000; 74:2239-2246], but it is consistent with Applicants' results thatshow that the MPER and smaller peptides from the MPER regions canfunctionally substitute for the Stem (see, e.g. FIG. 14).

Taken together, these results show that achieving significant expressionof G-Stem fusion proteins in infected cells and on virus particlesrequires optimization of the Stem domain. Applicants' finding that theNS Stem domain is perhaps optimal for expression of HIV MPER probablyreflects the fact that the MPER has Stem-like properties. Other antigensexpressed as G-Stem-antigen fusions may require different lengths ofStem to be incorporated efficiently into cellular or viral membranes.

Example 4: Insertion of the HIV-1 gp41 Epitopes 2F5 and 4E10 into theMembrane-Proximal Region of the Vesicular Stomatitis Virus Glycoprotein

Broadly neutralizing antibodies against the HIV Env protein may bindepitopes on gp120 and gp41 (see, e.g., FIG. 1B). Such antibodiesinclude, but are not limited to, PG9 and PG16 (which bind the base ofV1/V37372 loops and are trimer-specific), 2G12 (which bindscarbohydrates), b12 (which binds the CD4-binding site) and 2F5, 4E10 andZ13 (which bind the membrane-proximal external region (MPER)).

A schematic of VSV is presented in FIG. 2. VSV is an enveloped,negative-strand RNA virus of the Rhabdoviridae family. VSV infects humancells, but is not pathogenic and propagates robustly in vitro and is asafe and immunogenic vector for conducting animal studies.

A schematic of the VSV glycoprotein G is presented in FIG. 3. VSVglycoprotein G is a single envelope glycoprotein on the viral surfacethat forms trimers (ca. 1,200 molecules arranged as 400 trimers). VSVglycoprotein G mediates attachment, fusion, and entry of VSV into hostcell, accepts insertion of short amino acid sequences at certainpositions and has a membrane-proximal ‘stem’ region that sharessimilarities with the MPER of HIV-1 gp41.

Glycoprotein G is envisioned as an insertion site. In particular,epitope sequences, in particular HIV epitope sequences, more preferablyHIV gp41 2F5 and 4E10 epitope sequences may be inserted into the stemregion of VSV G. Replication-competent, recombinant VSV containing themodified G protein may be generated for use as an immunogen. FIG. 5presents a schematic of insertion and substitution of HIV gp41 2F5 and4E10 epitopes. FIG. 6 depicts insertion and substitution of the 2F5 and4E10 epitopes. For an insertion, the 2F5 epitope and flanking residueswas added to the VSV G stem region. For a substitution, residues in theVSV G stem region were replaced by the 2F5 and/or 4E10 epitopes. Asummary of the VSV G constructs are presented in FIG. 7. The expressionvector was pCI-Neo (deltaT7).

A Western blot demonstrating the expression and antibody recognition ofVSV G proteins expressed from plasmid DNA constructs is presented inFIG. 8. VSV constructs were expressed transiently in 293T cells and theWestern blot was performed with lysates (2% CHAPS). The Western blotshowed that the stem region of VSV G tolerated the insertion of the 2F5and/or 4E10 epitope, and that modified VSV G constructs were detected bythe 2F5 and 4E10 antibodies.

Trimerization of VSV G on the cell surface is presented in FIG. 9. TheVSV G plasmid DNA constructs were expressed in 293T cells, chemicalcrosslinking was performed with DTSSP(3,3′-Dithiobis-[sulfosuccinimidyl-propionate]) on intact cells andwestern blot with cell lysates was performed. As shown in FIG. 9, allVSV G variants form trimers on the surface of 293T cells.

Cell surface expression of VSV G constructs is presented in FIG. 10. TheVSV G constructs were transiently expressed in 293T cells, and flowcytometry was performed 24 hours post-transfection. The modified VSV Gconstructs were expressed on the cell surface and detected by the 2F5and 4E10 antibodies.

VSV G mediated cell-cell fusion is presented in FIG. 11. 293T cells weretransfected with plasmid encoding VSV G, briefly exposed to pH 5.2 after24 hours, and syncitia formation was observed. As shown in FIG. 11, VSVG-2F5-Sub and VSV G-4E10-Sub both induced cell-cell fusion. In addition,VSV G-2F5-4E10-Sub showed small areas of cell-cell fusion in rare cases.It was postulated that the modified G proteins may confer virus entry.To answer this question, a lentivirus reporter system was developed.

A lentivirus reporter system is presented in FIG. 12. 293T cells wereco-transfected with reporter plasmids pV1-GFP or pV1-Luc (HIV proviruswith 5′ and 3′ LTR), and plasmids coding for Gag-Pol and VSV-G.Supernatants containing GFP or luciferase-encoding lentivirusespseutodypted with VSV G were harvested, followed by infection of nalve293T cells. If VSV G mediates entry, cells will express GFP orluciferase.

Infectivity of lenviruses pseudotyped with VSV G is presented in FIG.13. 293T cells were infected with recombinant GFP-lentivirusespseudotyped with VSV G variants. As shown in FIG. 13, the infectivity ofVSV G-2F5-Sub and VSV G-4E10-Sub was similar to wild-type G.

Infectivity of reporter lentiviruses pseudotyped with VSV G is presentedin FIG. 14. 293T cells were infected with recombinant Luc-lentivirusespseudotyped with VSV G variants. Lentiviruses pseudotyped with VSVG-2F5-Sub and VSV G-4E10-Sub retained 33% and 35% of infectivitycompared to wild-type VSV G. It was postulated that these viruses beneutralized with the 2F5 and 4E10 antibodies.

Neutralization of lentiviruses pseudotyped with VSV G is depicted inFIG. 15. Luc-lentiviruses pseudotyped with VSV G-2F5-Sub or VSVG-4E10-Sub were incubated with 2F5 or 4E10 antibody at variousconcentrations. Subsequently, 293T cells were infected with theLuc-lentiviruses, followed by assaying luciferase activity at 3 dayspost-infection. Luc-lentiviruses pseudotyped with VSV G-2F5-Sub and VSVG-4E10-Sub were efficiently neutralized with the 2F5 and 4E10 antibody,respectively. It was then postulated that modified G proteins could beincorporated into recombinant VSV.

Recombinant VSV containing the gene coding for G-2F5-Sub, G-4E10-Sub andG¬2F5-4E10-Sub were rescued. A growth curve analysis by plaque assay onVero cells (m.o.i of 5) is shown in FIG. 16. The growth kinetics of rVSVcontaining G-2F5-Sub, G-4E10-Sub or G-2F5-4E10-Sub were similar towild-type. It was then postulated that rVSV G-2F5-Sub, rVSV G-4E10-Suband rVSV G-2F5-4E10-Sub could be neutralized with the 2F5 and 4E10antibodies.

Neutralization of recombinant VSV with various antibodies is shown inFIG. 17. 5000 pfu rVSV G-2F5-Sub, rVSV G-4E10-Sub or rVSV G-2F5-4E10-Subwere incubated with VI-10 (control antibody against the ectodomain ofVSV G, i.e. it should neutralize all viruses with G), 2F5 or 4E10 atvarious concentrations, followed by a plaque assay on Vero cells. Asshown in FIG. 17, rVSV containing G-2F5-Sub, G-4E10-Sub orG-2F5-4E10-Sub was efficiently neutralized by the 2F5 and/or 4E10antibodies.

To summarize this Example: (1) the ‘stem’ region of the VesicularStomatitis Virus (VSV) glycoprotein tolerated the insertion of the HIV-1gp41 2F5 and 4E10 epitope sequences, (2) the modified VSV G proteinswere expressed on the cell surface and detected by the respective HIVbroadly neutralizing antibodies, (3) lentiviruses pseudotyped with VSVG-2F5-Sub or VSV G-4E10-Sub were infectious and could be neutralizedwith the 2F5 and 4E10 antibody, respectively and (4) recombinant VSVswith G-2F5-Sub, G-4E10-Sub or G-2F5-4E10-Sub were infectious, hadsimilar growth kinetics like wild-type rVSV, and could be efficientlyneutralized with the 2F5 and 4E10 antibodies. Applicants conclude thatthe HIV-1 gp41 2F5 and 4E10 epitope sequences were presented in anative-like conformation in the ‘stem’ region of the VSV glycoprotein.

Example 5: Optimization Strategy adopted for optimization of VSV GProtein Coding Sequence

The gene was optimized for expression in eukaryotic cells using thefollowing steps:

-   -   1. Started with amino acid sequence for VSV G serotype Indiana,        strain Orsay (Genbank M11048.1)    -   2. The amino acid sequence was reverse-translated using the        OPTIMIZER webtool (available on the OPTIMIZER website associated        with Universitat Rovira i Virgili (URV)) and a human codon        frequency table [Puigbò P et al. Nucleic Acids Res. 2007 Jul;35        (Web Server issue):W126-31]    -   3. The DNA sequence obtained from reverse-translation was        scanned for potential mRNA splice donor and acceptor sequences        using the Splice Site Prediction webtool available on the        fruitfly.org website [Reese M G et al. J Comput Biol. 1997        Fall;4(3):311-23]. Potential splicing signals were disrupted        subsequently by introducing one or two synonymous codons, which        altered key elements in the donor or acceptor site. Synonymous        codons were selected based on frequencies found in the Codon        Table published by Zhang et al [Hum Mol Genet. 1998 May; 7        (5):919-32] for GC-rich transcripts.    -   4. The reverse-translated sequence also was scanned for        homopolymeric sequences ≥5 nucleotides. Those that were ≥5 were        interrupted by substitution of sequence with a synonymous codon        as described in the step above.    -   5. The sequence was scanned for the presence of mRNA instability        elements [Zubiaga A M et al. 1995, Mol. Cell. Biol. 15:        2219-2230]. None were found.    -   6. Optimal translation initiation (Kozak element [Kozak M. J        Biol Chem. 1991 25; 266 (30):19867-70]) and termination signals        [Kochetov A V et al. FEBS Lett. 1998 4;440(3):351-5] were        introduced.    -   7. Unique XhoI and NotI sites were added to the 5′ and 3′        termini, respectively, as presented in FIGS. 28A and 28B.

The invention is further described by the following numbered paragraphs:

-   -   1. A recombinant vesicular stomatitis virus (VSV) vector wherein        the gene encoding the VSV surface glycoprotein G (VSV G) is        functionally replaced by HIV Env.    -   2. The vector of paragraph 1 wherein the HIV Env is recognized        by antibodies PG9, PG16, 2G12, b12, 2F5, 4E10 or Z13, or other        Env-specific antibodies, including broad potent neutralizing        trimer-specific antibodies.    -   3. A recombinant vesicular stomatitis virus (VSV) vector        encoding a modified form of VSV G, wherein the modified form of        VSV G harbors epitopes from the HIV Env membrane proximal        external region (MPER).    -   4. The vector of paragraph 3 wherein the MPER sequence is        inserted into the membrane proximal region of VSV G.    -   5. The vector of paragraph 3 or 4 wherein a G-MPER protein binds        with high avidity to 2F5 and 4E10 monoclonal antibodies.    -   6. A recombinant vesicular stomatitis virus (VSV) vector        encoding a an N-terminally truncated form of VSV G (G/Stem),        wherein the G/Stem presents Env epitope sequences on the surface        of VSV particles.    -   7. The vector of paragraph 6 wherein G/Stem contains a        cytoplasmic tail (CT) and trans-membrane (TM) spanning domains        of G, a membrane proximal extracellular polypeptide (the Stem)        that can be 0 to 16 to 68 amino acids in, wherein HIV Env        epitopes are appended to the Stem.    -   8. The vector of paragraph 7 wherein the HIV Env epitopes are        MPER epitopes.    -   9. The vector of paragraph 8 wherein the G/Stem-MPER molecules        bind to 2F5 10 and 4E10 monoclonal antibodies with high        affinity.    -   10. The vector of any one of paragraphs 1-9 wherein the HIV Env        is a mutant HIV Env.    -   11. A method of generating novel chimeric EnvG molecules        expressed and incorporated into VSV comprising:        -   (a) serially passaging replication-competent chimeric            VSV-HIV viruses that lack the capacity to encode wild-type G            and are dependent on EnvG for infection and propagation on            cells to promote emergence of viruses with greater            replicative fitness and        -   (b) identifying novel mutations that enhance Env or EnvG            function.    -   12. The method of paragraph 11, wherein the cells are CD4/CCR5⁺        cells.    -   13. The method of paragraph 11 or 12 wherein the novel mutations        escalate trimer abundance on the virus particle and/or increase        the stability of the functional trimeric form of Env or a        chimeric EnvG.    -   14. The method of paragraph 11, 12 or 13 further comprising        determining whether the Env or EnvG immunogens elicit broadly        neutralizing anti-Env antibodies.    -   15. The method of paragraph 11, 12, 13 or 14 further comprising        applying selective pressure to generate novel Env or EnvG        molecules expressed and incorporated into VSV, wherein the        selective pressure is binding to an antibody of interest.    -   16. The method of paragraph 15 wherein the antibody is is PG9,        PG16, b12, 2G12,2F5 or 4E10 or any other broad potent        neutralizing Env trimer specific antibody.    -   17. A method of producing an immune response comprising        administering to a mammal the vector of any one of paragraphs        1-10.    -   18. A method of eliciting an immune response comprising        administering to a mammal the vector of any one of paragraphs        1-10.

Having thus described in detail preferred embodiments of the presentinvention, it is to be understood that the invention defined by theabove paragraphs is not to be limited to particular details set forth inthe above description as many apparent variations thereof are possiblewithout departing from the spirit or scope of the present invention.

What is claimed is:
 1. A recombinant vesicular stomatitis virus (VSV)vector wherein the gene encoding the VSV surface glycoprotein G (VSV G)is functionally replaced by HIV Env.
 2. The vector of claim 1 whereinthe HIV Env is recognized by antibodies PG9, PG16, 2G12, b12, 2F5, 4E10or Z13, or other Env-specific antibodies, including broad potentneutralizing trimer-specific antibodies.
 3. A vaccine comprising thevector of claim
 1. 4. The vaccine of claim 3, wherein the vaccine is anintramuscular or mucosal vaccine.
 5. A method of producing an immuneresponse or eliciting an immune response against HIV comprisingadministering to a mammal the VSV vector of claim
 1. 6. The method ofclaim 5, wherein the HIV Env is recognized by a PG9, PG16, 2G12, b12,2F5, 4E10, Z13 or a broadly neutralizing trimer-specific antibody. 7.The method of claim 5, wherein the vector is administered to a nasaland/or oral cavity.
 8. The method of claim 5, wherein the vector isadministered over a vaccination schedule from about 0 to 8 weeks.